Yes, this is along the lines of what I have done.  I would genuflect before the altar, with the intention of genuflecting before the Blessed Sacrament if or in case Our Lord is present, otherwise to relics in the altar and/or the altar crucifix.  Even when Mass is offered before an empty tabernacle, the altar servers still genuflect as directed by the rubrics.  There's the added consideration, if there are people present, that I would not wish to cause scandal to those who might be in there by refusing to genuflect to what they believe to be the Blessed Sacrament.  While I consider them to be in positive doubt, I also do not have certainty regarding the matter, so I prefer to give the benefit of the doubt towards reverence, even if in my mind I harbor mental reservation and conditionally redirect my reverence to the altar or the crucifix.

Similarly, I address Novus Ordo priests as "Father," for the same reasons, even though personally I hold the opinion that their orders are doubtful and even likely invalid.

Some argue that, well, if Our Lord is not present, then it's idolatry to genuflect.  Yes, materially and objectively, but not formally, since there is no intent to worship anyone or anything other than Our Lord.  So, too, if a person is mistaken materially regarding the presence of the Blessed Sacrament (e.g. thinks that Our Lord is there but is mistaken, say if a priest has removed the Blessed Sacrament but forgotten to extinguish the sanctuary lamp), that too would be material "idolatry" ... but nothing approaching formal idolatry.  That is not the same as genuflecting to a Pachamama by any stretch.  We're not the Prots who claim, for instance, that kneeling before a statue of Our Lord is idolatry.  Even the image or the thought or the concept of Our Lord is worthy of our reverence on account of Whom they represent, and the worship is directed toward the one Whose image is presented.  That's like claiming if someone kisses the picture of their mother, they're actually showing affection for a piece of paper, rather than for their mother.

In any case, IF Our Lord is indeed present, I dare not NOT genuflect before Him.  Yet, if He is not there, it could be material idolatry.  So in either case, you could be doing something inappropriate (objectively or materially).  But I'd rather genuflect toward an altar/crucifix than to refuse to show the required reverence to the Lord God.

EDIT:  that statement about people worshipping an empty tabernacle reminds of the time that Father Pfeiffer attacked Father Chazal for allegedly doing this on purpose:

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I don't genuflect to Novus Ordo tabernacles. However, I do occasionally visit cathedrals and I will kneel before the statues of saints, light candles, and pray. But I don't bless myself with their (non)holy water and I don't genuflect to their empty tabernacles. I suppose I should bow.

And part of my stance is that I don't feel personally qualified to judge whether the New Mass is valid or not as a layman with no status in the Church.

The responses to this question are fascinating!

The answers epitomize the traditional Catholic schizophrenia Bp. Williamson mentioned in his RTF interview last Thursday.

So wouldn't that work for both the validity of the consecration at the NO mass as well as the validity of the host in the tabernacle? 

But the Novus Ordo is not a Black Mass nor an Orthodox liturgy.  The issue brought up here was that we can not know whether the Novus Ordo is certainly invalid/not Catholic.  So, why would we genuflect but not assist there? Wouldn't avoiding the NO mass also be disrespectful to Our Lord?  After all, He may be on that altar. 

And part of my stance is that I don't feel personally qualified to judge whether the New Mass is valid or not as a layman with no status in the Church.

"Here is the error of our Protestant friends. They recognize no distinction between reason and private judgement. Reason is common to all men; private judgement is the special act of an individual …. In all matters of this sort there is a criterion of certainty beyond the individual, and evidence is adducible which ought to convince the reason of every man, and which, when adduced, does convince every man of ordinary understanding, unless through his own fault. Private judgement is not so called … because it is a judgement of an individual, but because it is a judgement rendered by virtue of a private rule or principle of judgement …. The distinction here is sufficiently obvious, and from it we may conclude that nothing is to be termed ‘private judgement’ which is demonstrable from reason or provable from testimony."

(Brownson’s Quarterly Review, October 1852, p. 482-3. Emphasis added.)