Previously we have shown that the default in our tradition is that the narratives of the Torah are to be taken literally and any allegorical truth is in addition to the pshat. We have noted that additional apparent age is a logical necessity from the literal account of B'reshis and not just a speculative possibility. We have also seen that the common decent of man from our common ancestor Adam is a fundamental principle and argued that even according to the more liberal standard of the Rambam it may not be permissible to reject the literal meaning of a Torah passage without deductive proof.
I would like to pause to re-emphasize the significance of this last point. In order to discuss the propriety of allegorizing the Torah we must accept for the argument that there is good reason to believe it to be Divine Revelation and therefore true. Otherwise in the absence of such reason there is no justification for allegorizing an account that has no indications it is merely a metaphor, but rather we would logically conclude it was simply an erroneous account. [Recently a commenter at another blog argued that there was textual basis to understand the account allegorically in the term "day" being used before the creation of the sun. When I pointed out that "day" was largely understood literally, he responded that a couple hundred years ago that is how they probably would of understood it too!]
So accepting that the Torah is true, and recognizing that the burden of proof is on those who wish to say that truth is allegorical and not-literal, then we must recognize that B'reshis is essentially divinely revealed testimony about how the world was created. We also must recognize that God's general plan was that the world operate according to the laws of nature as we know them. If God has told us He created the world in a certain manner but to have done so would essentially require miraculous intervention in nature for it to be as it is today, it is an argument from silence to argue that God didn't make such interventions and therefore posit that His testimony is really allegorical.
Wolfishmusings.blogspot.com/2007/02/goodbye-gosse.html makes an argument that seems to be a very good way at "testing" the Apparent Age approach's ability to solve the difficulties. In it he points out that through genetics science can identify when a species most recently shared a single common ancestor and it is common that they have not shared a common ancestor since long before Adam HaRishon's time.
In the generations following the Mabul, but especially those from Adam HaRishon, would not have enough genetic variety to support a healthy population. The association between birth defects and relatives, especially siblings, reproducing has long been recognized. Divine intervention would not be a matter of hashgacha pratis, but merely of hashgacha klalis, a necessary measure for the healthy development of the species.
Conceding that such divine intervention took place, as we must from an account which on the one hand presents the origin of the species from at the most a handful of pairs and on the other is completely unconcerned with the long known and statistically significant chance of genetic defects from such unions, it is more reasonable than not that the genetic variation necessary would be correlated with the general plan He had for the biological laws of nature. Again, while the account does not explicitly elaborate on such an intervention, it is a necessary condition for the simple meaning of the account even based on a pre-modern understanding of the reproduction of close relatives. And if something is inferred by necessity by the simple meaning then evidence which it can account for does not provide sufficient reason to allegorize the account.
Now it is all well and good to argue that apparent age is a logical necessity for the simple meaning of the text, and that divine intervention in the gene pool is also a logical necessity. It is not, however, logically necessary that there be a correlation between apparent age and genetics. But neither is there correlation an argument for allegorization. And while it is not logically necessary, insofar as the world was created as a way to conceal God to allow for free will, the alignment of the physical evidence in a [generally] unified and coherent scientific/materialistic system, despite several directly supernatural occurrences, is understandable if not expected.
I hope to elaborate/explore the role of free will's relevance to the natural world more thoroughly later, as well as the relationship between the teivah/nature as God way of running the world and it's applicability to the pre-Creation era/Retroactive Existence.
I do not mean to make light of the challenge this argument presents, but starting with the assumption that we have reason to believe that the Torah is God's account of Creation I do not believe the challenge is sufficient to disregard it. And if we remember that, insofar as common ancestry via Adam HaRishon is a "fundamental principle" which cannot be allegorized if there is any other alternative even according to the Rambam, the theoretical possibility of divine intervention negates the basis to allegorize even without the above reasons to infer it occurred. The conclusions of genetics are immanently reasonable inferences from the scientific evidence, not deductive/demonstrable proof of what occurred.
The Rambam warns that if one, "reject[s] things as impossible which have never been proved to be impossible, or which are in fact possible, though their possibility be very remote, then you will be like Elisha Aher; you will not only fail to become perfect, but will become exceedingly imperfect" (Guide 1:32, Freidlander page 42, emphasis mine).