What is left after the reduction is complete? Some irreducible objects (the Greek word is atom) and what? Why do these "atoms" behave the way they do? Are the rules of atomic behavior part of the Nature? Or of our description of it?
I strongly suspect that what is left is not an irreducible "object" in the common sense, but rather that the part about how these atoms behave the way they do is all that is left after a fully complete reduction. No object-style "atom", only the behavior. The behavior is the atom.
Does that help?
Basically, the way I understand it, you don't reduce to quarks and leptons, and then wonder "But how oh how do these quarks do this and that? Why do they do it?". Instead, you reduce to the wave function, and there is no quark left, a...
If it's worth saying, but not worth its own post, even in Discussion, it goes here.