Actually, it's good rather than bad philosophy that recognizes your equivocations. Our species is natural in some ways and not in others, since "natural" has many meanings.

The article here sketches the relevant sense of "natural" that applies to animals rather than to people: being subject to the niches in a given, wild environment. What's unnatural, then, is creating artificial, intelligently designed and thus not wild environments, such as civilizations, and adapting ourselves to them.

Who's "discounting human capabilities"? That's a strawman.

The kind of freedom (self-control) I have in mind is compatible with metaphysical determinism.

My account emphasizes what's amazing about people since I don't overlook our anomalousness. Certainly, we come from nature, but nature-as-wildness undoes itself and adds levels of complexity to itself. Artificiality emerges from wildness, and the former isn't reducible to the latter.