This won’t handle all the features you are discussing but a year ago I spent a few weeks hacking this Python code to bake (and delete) geometry by layer with custom materials:
Introduced and explained at greater length a few weeks earlier:
It was agony digging through the forum (ten years of requests for this capability!) and the Rhino APIs.
It works well enough for me but someone who knows what they’re doing might be able to take it further. There is no indication from McNeel that they plan to do this or even understand the need for it.
