I don't have any references, but I'll share my view:
The way the particles are actually behaving is part of the territory, the mathematical symbols we use to describe such behavior are part of the map.
And I don't see how this calls the whole idea of reductionism into question. In fact, if the behavior of such particles can be described using a simple mathematical formalism, in my opinion, that is reductionism at its finest. We have reduced the apparently complicated motion of, for example, a dog, into the movement of particles according to simple formulas. Simple mathematically describable behavior patterns, though non-physical (if you insist on categorizing them that way), are not magic.
I feel as if I may be missing the point, because I didn't become confused after reading your questions. Please clarify, if I did miss the point.
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?
If it's worth saying, but not worth its own post, even in Discussion, it goes here.