Dear Sylvia,
Thank you for reading my essay and for commenting on it.
The answer to your worry is in the last page of the essay, point (C): namely, in the distinction between Quine's and Aristotle's ontological projects. I quote from the essay: 'the worlds that I have been describing are not to be (naively, and wrongly!) identified with the world as it is in itself--whatever that might be taken to mean.'
Working out the ontology of scientific theories, the way they are interconnected, and their logical structure, is a different project from explicating the way in which the elements of that ontology exist in our world--which is Quine's project not Aristotle's. Aristotle's project about 'being' differs from Quine's project about 'existence', in that the former allows for things, and categories, to appear in our ontology, that we may one day come to reject as literal parts of our world. Those things are, in some sense: even if they do not exist in the literal sense in which the theory would say they do.
This is how my framework avoids Whitehead's fallacy of misplaced concreteness. Whitehead also says something else in that first masterly chapter of Process and Reality: namely, that the accurate expression of the final generalities is the goal of the discussion and not its origin. This is the spirit in which I have undertaken this ontological project: for it aims to investigate how things are, according to our best scientific theories, rather than explicating their existence in our world. That second, more ambitious, Quinean project needs to be undertaken, for sure: but I believe that one should be not too hasty about the latter. For there are some important questions about the ontology of emergence and reduction that need to be addressed before that more ambitious project can be undertaken. This is what I have done in this essay.
Best,
Sebastian