@jeeprs,
Not to be wishy-washy, but it seems like the two halves of this debate are not really communicating. Both seem like they have some valid points. Leaving aside for the moment the veracity of scientific claims, the question at hand seems to me to be the truth value of statements claiming an ontologically a priori status. But please correct me if I am wrong.
Coming at it from the ontologist's perspective, one cannot reasonably ascertain such a truth value, because the a priori statement itself provides the very conditions for the possibility of truth (or falsity, for that matter.) Truth and falsity are claims made a posteriori, and a priori postulates are not subject to them. If a priori claims cannot be found to be untrue, they may, however, be an insufficient premise upon which to ground further conclusions regarding ontic facts. They may also be found to be in contradiction with other a priori claims, but I don't know that even this theoretical contradiction makes them untrue. Take, for example, Kant's idea of the "thing-in-itself." I think that even Kant wanted to explain it away, but it was too convenient a concept to be dismissed. It is only necessary to prevent several other a priori claims in his critique from becoming contradictory. (Forgive me, I am exhausted, and this point is undoubtedly debatable. I have no interest in defending it.)
On the other hand, following the line of thought Nietzsche lays out in
Twilight of the idols, philosophers have a tendency to place last things first. Ontological postulates are, let's say for argument's sake, large generalizations arrived at by making a number of observations and assumptions about ontic phenomena. The relevance of the ontological claim will depend upon the value of the perceived order upon which it is based. An ontology assumes, in some way that the order of things seen is determined by principles unseen, and then speculates as to those principles. Ontological postulates assume, to some extent, the veracity of that order. But if additional historical details arise that disprove the integrity of that assumed order, then I would say that the principles in question are no longer relevant. Think of it this way, one could claim that new scientific observations of how biomes operate makes a Medieval description of the Great Chain of Being irrelevant without disproving anything.
