Hypothetically, science proves free will isn't real

[Neo-Scholastic]

Weren't you the one who quoted Aquinas that there is nothing in the mind which doesn't first appear in the senses? You seem to be shifting your argument.

You may be confusing Aquinas’s epistemology with his ontology. Knowledge of a thing still depends on its prior existence.

… it is not possible for reason to overcome its limits no matter what your existential commitment…there is no way to tell if we are or are not at the last layer of the onion. It could go on further for all we know. Your commitments don't resolve that quandary. Reason, ultimately, cannot provide justification for itself.

Not sure if we are debating whether human beings imperfectly apply reason or whether reason itself is faulty. I agree that humans are flawed beings, but I say that we can overcome those flaws with reason. Do you doubt this? I also believe that first-principles are truly self-evident. You seem to be suggesting that they may only appear to be self-evident. If first principles are up for grabs then pretty much everything is. Do you disagree?

… your argument that these paradoxes and seeming absurdities are a problem is at heart an argument from ignorance…

Paradoxes serve as indications that something is wrong with the theories that produce them. In the absence of a plausible theory, one that doesn’t resolve the paradox, more inquiry is required. But that’s not what’s happening here. These are not questions that yield to empirical findings. Some lines of reasoning are true dead ends. Moderate realism avoids paradox whereas the known alternatives do not. It makes no sense to reject a plausible theory when there is no good reason to oppose it, just because you think someday, maybe an undiscovered alternative will appear to redeem your doubt.