Its possible that we simply havent evolved yet the mental faculties to reconcile them. After all none of these theories were around even like 200 years ago - we had in fact no clue whatsoever about any of that stuff. Mathematics is an evolving process and it can make leaps. The current knowledge might be like distinct coordinate patches on an underlying manifold that we will asymptotically cover with a consistent collection.

On the other hand it may indeed be a remarkable feature of the human mind that it can "make mathematical sense" of subsets of reality, but there is no overarching system and no reason to expect that we will be able to make simultaneous mathematical sense of "everything".

It might take a long time to collect sufficient such "metadata" to help tilt the balance.