I agree. Unless you reject John XXIII as pope, AND Pius XII, then you have to accept the genuflection and the removal of perfidious. This is part of the 62 missal, which is a revision of Quo Primum. However, the changes made in 2008 by +Benedict to the 62 missal I think are non-binding, because he made these changes, legally, as part of his motu, and not as a revision of the 62 missal/Quo Primum. I don't think such changes are legally in force.
If I recall, the second Confiteor was dropped in the 1962 Missal. But the SSPX put it back in. So do you follow the 1962 Missal or do you not?
We had a thread on this a few months ago, and Drew was involved with explaining the history of the 62 missal; it's quite complex. Basically, John XXIII issued the 62 missal, ordinary form, which mainly updated the calendar and confirmed the 1955 Holy Week changes. This first edition did NOT delete the 2nd confiteor, nor did it have the addition of St Joseph to the canon. So, in my opinion, these changes are not part of the 62 missal. Between the years 62-65, there were "supplemental" changes to the 62 missal, none of which mentioned Quo Primum in their laws, so this shows they are not really part of the 62 law.
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In fact, if you go out to order a 62 missal on-line, there are some which have the canon intact (with no St Joseph) and they provide you with a sticker to place over the prayer, in order to add his name, because this was a "later" change, after the original 62 edition was already printed.
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I think this is why +ABL kept the 2nd Confiteor and other minor things. Because he accepted the original 62 missal but not the supplemental add-ons. This makes sense to me.