This was painful to read. Do not all metaphysical position derive from science or what could be called proto-science, i.e. observations of world and its processes at various levels of precision? It's only natural (pun intended) that naturalist will have the upper hand and a more precise picture (even if clearly incomplete).

After all, if you derive your philosophy from modern science, you can at least acknowledge (and look out for) when bias and/or projection creep in. Alas, theists obviously (and unironically) build their philosophies on biased observations and subsequent psychological projection. One may even say that that bias and projection are deliberate building blocks of theistic metaphysics. Makes one wonder, why.

Also, how could God be not natural? Naturalism could as well be called causalism -- it derives its philosophy from observation of causal chains. So, even theism with God as "primal cause" is merely a different kind of naturalism. And of course, miracles may turn out to be completely natural, i.e. causal (just extremely improbable).

And so on and so forth...