So I think what I would say is that the setting is agnostic with respect to the correct ontology, so having a particular ontology isn't a valid reason to reject it.
E.g., if your ontology divides the world into aspects like Quantitative, Spatial, Kinematic, Physical, Biotic, Sensitive, et cetera, then consciousness may just be a boundary around a bunch of things rather than a "natural" or "fundamental" kind. But it still exists, so you should still be able to say e.g. whether or not it has causal effect. (And the case that it doesn't exist at all is also covered; that's illusionism.)
Same for atoms. if your ontology doesn't deal in terms of atoms, that just means atoms are a boundary around a bunch of other things, but they're still there. Unless you think atoms don't exist, in which case that's subjective idealism.