What I object to is reductionism in principle. Logic can work in a "reduced" system. But to the extent the system is reduced, the applications of logic must be reduced to the size of that system. Logic all by itself will not propose questions outside its specifically directed application.
And system "sizes" are determined according to the way in which they are defined and modeled. If all your modeling is conducted on the presupposition that the only thing that ultimately exists, is "matter in its motions," then you necessarily have an extremely reduced model of the natural world. Logic can still work there; but it can never give you the "whole story."
Perhaps the most important part of the "whole story" that is edited out in this process is what Einstein called "'free creations of the human mind,' on which he believed science depends." [Rosen, ibid.]
Heck, on the widely-accepted materialist/mechanistic models, the human mind itself must be held suspect as something that really is a fiction (since we can't "observe" it). And yet science depends on it; for without mind, science cannot do its work.
Do you not see the inherent logical self-contradition at work here?
Yes but I don't see any solution being offered. Reductionism eliminates information that cannot be conveyed. You protest that this is too limiting, but can't explain how to make it work without it.
In a perfect world we wouldn't have the physical limitations we do. But it is what it is, and our choices are to do it the best we can within the limitations we have to live and work with, or not do it at all.
I choose the former.