I was speaking in generalities.  Logic.  Science.  Facts.  Take your pick.
An outcome cannot be certain when an input is presumed.

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Presumed=converted to morally certain.
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To say intention is presumed is not to say "well, I'll never know, I'll just presume he intends to make a sacrament happen."  To say intention is presumed is to say "Given that men act as they think, and this man is acting in the only way by which it is possible to confect a given sacrament, I presume he intends to act this way, and therefore am morally certain that he has the required intention."
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But to take the "invisibility" of intention and, from that, conclude we cannot be (morally) certain about intention is wrong.  If we are not morally certain about intention, then we can't partake in the sacrament. 
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The reason that the language is that we presume intention is that intention is internal.  We can actually see/hear that matter and form are correct and present, so there is nothing to presume in regard to those elements.  We cannot see intention, we can only see indicators of it (mainly, the presence of matter and form correctly applied). But in the presence of those indicators, we presume that the intention is there, and that presumption itself is controvertible with moral certainty.  So don't let the language throw you off. 

I guess you could say there are two intentions that need to be formed.  One is the intention to form the correct intention.  And the other is to perform the ceremony correctly.  If the ceremony is performed correctly then it is certain that the intention was also correct.  The only way the intention could not have been correct was if there was an external sign.

Jaynek cited Cardinal Billot on another thread:

The intention of doing what the Church does, whatever that may be in 
the opinion of him who administers the sacrament, is said to be required. 
Thus St. Thomas: "Although he who does not believe that baptism is a 
sacrament, or does not believe that it has any spiritual power, does not 
intend when he baptizes to confer a sacrament, nevertheless he intends to 
do what the Church does, even if he counts that as nothing; and because the 
Church intends to do something, therefore, as a consequence of this, he 
intends implicitly to do something, though not explicitly."[1] But it is 
not necessary that the minister think as the Church does, or that he not 
err concerning her teaching; for it is enough if his intention is towards 
something which is identically that which the Church intends, or, something 
which amounts to the same thing, for example, if he intends to do that 
which Christ instituted, or which is commanded in the Gospel, or which 
Christians are accustomed to do according to the prescription of their 
religion. (Thus it is apparent how even a Jєω or a pagan can have an 
intention sufficient for baptizing. Consider for example a catechumen 
placed in a moment of necessity, who asks a pagan saying, "Do for me, I 
entreat you, this mercy, that you pour water on me, pronouncing the words, 
'I baptize you,' etc., with the intention of doing what I myself intend to 
receive according to the prescription of the law of Christians.)

I haven’t studied sacramental theology much so I don’t know about what constitutes moral certainty about the intention of the minister but it seems to me that it should be theoretically impossible for a minister to deceive the public about his intention.  How can you have an intention to not do what the Church does when you have an intention to appear to be doing what the Church does?  The only way I can think of to do that is to not be a valid minister but only to appear to be a valid minister.  Otherwise, I don’t see how a valid minister could form the intention to deceive without actually having the intention to do what the Church does. It is possible to perform the ceremony without intending to do what the Church does but only if you publicly state your intention so that you aren’t actually doing what the Church does.  If you don’t state it publicly then you actually did do what the Church does and even if you didn’t initially intend to do what the Church does, you ended up doing what the Church does intentionally.

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That's an interesting way of looking at it, although I don't think sacramentalists look at it that way.  They always admit the possibility of sacrament simulation (something most moralists at least touch on).  Theoretically it is certainly possible, and grievously sinful, of course.  Maybe a decent way to think about how it can be possible is to think about the Church's marriage laws.  One cause for nullity of marriage is when consent is lacking-- not the Novus Ordo "they didn't know what they were getting into" type way, but in the real and substantial way: someone who says "I do" while very explicitly, at the same time, saying "I don't" internally. 
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Now, marriage is a sacrament, the validity of which is the responsibility of the marrying couple.  Withholding intent to marry is synonymous with withholding intent to baptize or any other sacrament.  And the Church recognizes, indeed even builds into her law, the possibility for intent to be explicitly withheld despite the outward appearance.  So I think we can't get very far contending that it is theoretically impossible to withhold intent.
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Of course, in the moral order of things, one shouldn't be scrupulous about such "possibilities."  The reason these "possibilities" even cause problems to begin with is that modern man, including modern Catholic man, is accustomed to thinking materialistically-- he thinks that there are things which are 100% certain (like the laws of nature or the laws of God) and then there are varying degrees of "not 100% certain."  But that's not how Catholic theologians have ever viewed certainty, as though it were a composite on a quantitative scale.  That's a modern corruption, and it might be suitable for empirical sciences, but it is not suitable for anything else, including daily-decisions of even the mundane variety.  Moral certainty is true certainty.  It's not 99%, 100%, 45%, etc. "type" certainty.   We should try our best to disavow ourselves of thinking of certainties in this way.

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That's an interesting way of looking at it, although I don't think sacramentalists look at it that way.  They always admit the possibility of sacrament simulation (something most moralists at least touch on).  Theoretically it is certainly possible, and grievously sinful, of course.  Maybe a decent way to think about how it can be possible is to think about the Church's marriage laws.  One cause for nullity of marriage is when consent is lacking-- not the Novus Ordo "they didn't know what they were getting into" type way, but in the real and substantial way: someone who says "I do" while very explicitly, at the same time, saying "I don't" internally.  
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Now, marriage is a sacrament, the validity of which is the responsibility of the marrying couple.  Withholding intent to marry is synonymous with withholding intent to baptize or any other sacrament.  And the Church recognizes, indeed even builds into her law, the possibility for intent to be explicitly withheld despite the outward appearance.  So I think we can't get very far contending that it is theoretically impossible to withhold intent.
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Of course, in the moral order of things, one shouldn't be scrupulous about such "possibilities."  The reason these "possibilities" even cause problems to begin with is that modern man, including modern Catholic man, is accustomed to thinking materialistically-- he thinks that there are things which are 100% certain (like the laws of nature or the laws of God) and then there are varying degrees of "not 100% certain."  But that's not how Catholic theologians have ever viewed certainty, as though it were a composite on a quantitative scale.  That's a modern corruption, and it might be suitable for empirical sciences, but it is not suitable for anything else, including daily-decisions of even the mundane variety.  Moral certainty is true certainty.  It's not 99%, 100%, 45%, etc. "type" certainty.   We should try our best to disavow ourselves of thinking of certainties in this way.

#38 and #39 was me.  I intended to check the box but I didn't.  Get it?  Actually, if truth be told, I never did intend to check the box.  I may have desired to check the box but I didn't intend to.  If I had intended to check the box, I would have at least made an attempt to click the box.  But I didn't even make an attempt.  My bad.  Could a murder suspect claim that he never intended to murder the guy?  Yes, he could but if the murder was accomplished by some elaborate scheme then the judge/jury will come to the conclusion that he actually did intend to murder the guy.  So while I agree that a sacrament can be simulated, I disagree that it could be simulated merely by having/entertaining a thought about simulating it.  In order to actually simulate a sacrament, you have to take some steps to achieve a simulation.  If you don't take any steps to achieve a simulation then you never actually intended to simulate it (even if at some point you desired to simulate it).  Performing a sacramental ceremony cannot be a simulation by default.  Rather, if all the external requirements for validity are met then it is valid by default.  The intention must have been there or it would not have happened as it did.  I think intention is a pretty low bar to meet.  On the other hand the form and matter have to be correct.  Have you ever heard a priest repeat the words of consecration?  I have.  It is disconcerting to think that a mispronunciation of Latin could invalidate the sacrament but it could happen if the mispronunciation is bad enough to change the meaning.  When I am serving I listen to the words but I don't worry about it because I also would not go to a Mass by a priest who was obviously incompetent or untrustworthy.  I think I would be very scrupulous about a baptism performed by a non-Catholic.  I would want to be absolutely certain that they used the correct form and matter.  But I would trust a good priest even if I was not a witness of the form and matter.

I agree that the bar is incredibly low.  I didn't mean to imply that I think sacramental simulation is at all common, or that it could occur inadvertently. Theologians say that even a virtual intention suffices.  I just meant to say that it is possible (to simulate a sacrament, i.e., to withhold intent purposefully, and willfully, despite the outward appearance of proper confection due to requisite form and matter).
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There's a (somewhat humorous) story about St. Athanasius.  When he was a boy he was playing on the land near the Patriarch of Alexandria's property (I believe that Patriarch was named Alexander).  Alexander looked out his window and saw a curious thing; a young man was officiating what looked like Easter baptisms.  He went down to see what was going on and asked the boy who was doing the officiating (this boy was St. Athanasius) if he was a Christian.  He said yes.  And he asked about the others, and Athanasius said they were Pagans, and that they were playing "Bishop" or some such thing.  Alexander asked Athanasius how he baptized them and Athanasius described the baptisms.  Alexander told him that he had really baptized them.  Athanasius was embarrassed and also shocked, since he thought only a bishop could baptize.  
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So there's an instance where someone intended to baptize, but didn't think they could (efficaciously).  Still valid.  Illustrative of the point (the low bar for intention).

Right, I agree mostly with what you say here.  But maybe I am misunderstanding you on the specific point of withholding intent despite the outward appearance of proper confection.  I think the St. Athanasius story is an illustration of how the outward appearance is the key to knowing the proper intent.  If the form and matter are correct and the minister is valid, and there is no outward sign that the intention is contrary then the sacrament is valid.  There can be no possibility of it being invalid.  The outward appearance is a manifestation of the intent.  To say otherwise is to say that the minister could form 2 contrary intentions for the same act.  That is impossible.  So priests have to be responsible about saying the words of consecration.  He can't go into a chapel and say a Mass and then afterwards say, oh, I didn't mean it, it was just practice.  He would have to give some indication beforehand that it was not intended to be a Mass.

That's an interesting example.  Athanasius was not intending to do BAPTISM ... was just simulating it or playing.  But he intended to perform the Church's ritual, to DO what the Church does when conferring Baptism. 

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Bingo.  Very interesting, isn't it?  Cuts right to the heart of the thing to illustrate in more operational terms what exactly intention is.
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Now, this was just Alexander's opinion of course, and he could have been mistaken.

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Yes, granted.