Upvoted; I like where (I think) this is going.

To your distinction between mereological and nomic reductionism, I would add a third kind of reductionism ("ontic reductionism" would be a good name) that goes beyond the mereological claim, to say that the only things that really exist are the entities of fundamental physics. In this view, quarks/strings/wavefunctions or whatever is posited in the ultimate theory are real, but high-level entities like trees and people are only "real": they are certain combinations of fundamental entities that we signal out for a convenient description.

I'd say that trees and quarks are both real, without qualification, and that the concepts of trees and quarks are part of maps we make, and that relations like "reducible to", more fundamental than", etc, all speak about maps and not territory. So to say stuff like "only quarks really exist" is a map-territory confusion, and what we ought to say is that the map involving quarks is more comprehensive, accurate, universally applicable, etc, that the map involving trees.

(It bugged me to no end in the "Reductionism" chapter of HPMOR that Harry seems to make this mistake, confusing his timeless quantum mechanics map with reality itself.)