Align with your general thesis, and it seems to me reasonably clear why we cannot ever rationalize anything completely.
If you do the numbers on us, we are really complex, far beyond our capacity to know in detail.
If you dig into quantum mechanics, it is probability based.
Heisenberg uncertainty sets fundamental limits on the degree to which anything may be approximated.
We now understand many classes of complexity that cannot be predicted and some that cannot even be approximated.
We now understand something of the complexity of what it is to be a human being from the systems perspective, and it is such an order of complexity that it is impossible for any human to ever understand their own motives, we are all necessarily far more complex than that.
It seems reasonably likely that reality is at base, rather than being strictly lawful, a balance between the random and the lawful (a form of constrained uncertainty) that very closely approximates causality in many contexts at our normal levels of perception.
Like you, I am a yes to using reason and logic as the best tools we have for building models of reality, and let us never confuse our models with the thing being modeled (that is a category error in logic).
Yes, things like love and beauty may be deeply encoded by evolution into our subconscious systems, and that doesn’t make them any less real or valuable.
Yes we have values we cannot consciously explain in great detail (yet we can always rationalize to ourselves and others), and that is a necessary part of the complexity embodied in being human, being a deeply complex highly evolved self aware (at least to the degree that we are) entity.
Any idea that reason actually tells us anything “True” about reality (rather than the more humble idea that all knowledge is a “useful approximation” at some level) seems to be an arrogant error in logic.