That's a rather bold claim. It implies that Catholic theologians are, among other things, uninterested in ethics, aesthetics, metaphysics, and epistemology, just to name a few other subjects of interest to philosophers. I'm frankly baffled that you would reach such a conclusion, but OK.
> Catholics are allowed to believe in atomism as an instrumental model, but not as the ultimate interpretation of how the Universe works
Well to be Catholic you have to believe in an ultimate eternal God, so ultimately we believe that everything in the universe is both created and sustained by Him and everything observable is some kind of instrumentality, be it evolution, quantum electrodynamics, or anything else. Nevertheless that doesn't in any pragmatic way restrict one's ability to form scientific hypotheses or theories. Indeed it's arguably closer to the Newtonian ideal of focusing on accurate description of phenomena.