I used "quarks" as a placeholder for whatever "fundamental" physical entities are posited as "truly real" by the reductionist. You seem to be using "waveforms" in a similar way, so I am confused as to whether we have a disagreement or not.

If the fundamental concept in physical theory is "waveform", then I'd say: there is a map in which you can describe all reality as waveforms. There is a map, less comprehensive but more useful for many purposes, in which you can describe some aspects of reality as trees. I don't like saying "Trees are special cases of waveforms" because it seems to place the reductionism at the ontic level (territory) instead of in the maps: it is a short distance from it to "only waveforms really exist", which I regard as confused.