Levi Bryant has been serial posting on naturalism for weeks, though this is a response to "I Guess My Ontology Ain't Flat".
For now, I would note a difference between pragmatic naturalism, including Peirce whom he references at length, and his materialistic naturalism. I would insist that qualities are not "in" or "outside" of "objects" or things. Phenomenal qualities come into being through interaction (kind of like his endo-qualities), while absolutely "intrinsic" qualities ... well ... there cannot be said to be any. That is, if something is intrinsic to a thing and never external, then we have nothing to say about them since they are essentially closed and private to all of nature. They are nominal, not universal, and thus cannot be discussed or communicated. They cannot be the subject of an ontology, unless one admits that one writes pure metaphysical fiction as opposed to transcendental or abductive arguments. In that case, one should write metaphysics like Rousseau writes ethics in his "Discourse on the Origin of Inequality"; he admits his fictions, but writes them for political expedience in his iconoclastic way. Or maybe he could take the Rortian route and call his metaphysics "edifying literature." But he will not.
Is my transcendental ontology flat? Sure. I think there's only nature. But why exclude spirit from nature? Why assume we know the line between the natural and supernatural? Why assume the natural is only physical? If we are indeed talking about what is "inside" objects, to which we have no access, then we're just making an ad ignorantum argument, are we not? Likewise, I'm not saying that there is a supernatural per se; I just do not reduce nature to my concept of nature.