On pragmatic, neo-Kantian grounds, I'd agree that our conceptual distinctions are always partly subjective, in that we "cut" the subject matter so we can understand it. But I think that that point applies to either substantive or relational ontologies. I'm not sure the issue is whether there are intrinsic, brute properties. There might also be brute relations, as in ones we can't further analyze. So that strikes me as a different issue. The question here might instead be whether we best understand phenomena by thinking of them pragmatically, half-subjectively as made up of just relations or relations between things. There's no need to assert that things consist of things all the way down.

I have an article coming out soon on whether the whole of nature can be understood scientifically as a natural thing.

The dichotomy between magic and infinity is an intriguing one, but I don't think it's coherent to speak of an "infinite whole." "Whole" implies finitude, as far as I can tell. In any case, "whole" wouldn't be part of the scientific theory.