So it appears that we need to bend our perception of reality to fit in with limited human scientific discovery.
Yes, essentially, that is what we need to do if we want to understand things with any depth beyond the merely superficial. It has been an overarching theme of science that how things
seem to us is not how they actually are in any objective sense. Most of our experience is illusory in some or other sense. How things seem is a product of our particular evolutionary pathways, all experience is construction of mind; that computer screen you are seeing right now is not actually the computer screen, it is a neurological fabrication constructed more from memory than from novel optical input, but it sure doesn't feel that way does it ? None of us experiences reality directly, as it is, nature has no remit or incentive to do that. Rather, what nature does is to create forms of experience that keep us alive and reproducing at minimum cost, we don't need to swim in full undiluted reality in order to navigate the world. That computer screen you are seeing might not be the real deal, but it is good enough to get us through the day; similarly with free will, it matters not for most intents and purposes that our decision making is ultimately determined, we feel free and that is good enough for daily living.
Can you not contemplate the possibility that our perception of reality may be correct, and a piece of rock does not have self awareness, and our free will is not driven by uncontrolled cause and effect chains, and we have yet to discover the true reality of how it all works?
Science is never finished, but it is unlikely that all our findings are going to be completely reversed, that would be inconceivable. So, we run with our current understanding, that represents the best current knowledge.