In this article I criticize new atheists for being rationalistic or scientistic, for their promethean or Luciferian presumption that all our beliefs should be rationally justified. That presumption is at best useful, given certain interests or goals; it's comforting in modern terms rather than itself being rationally justified.

You define atheism as the claim that supernaturalism should be rejected until it's rationally justified or until all the alternative rational explanations are exhausted. So you're assuming the above promethean rationalism. You're saying the atheist privileges reason, meaning that we should prefer rational explanations to nonrational stories.

The theist can say, then, that God enters the picture not just when there's a "gap" in rational explanations, but when reason runs out completely, such as when we're wondering whether the natural order itself, including all natural laws and beings is all there is or whether nature is non-naturally produced.

So when you say, "as far as we know, only the natural exists," you're talking about our limited experience on this planet. Why should those limitations apply to all beings in the metaphysical context? It's anthropocentric to ground your ontology in human experience, knowing that we're creatures that accidentally evolved. Who says we evolved to understand or to experience everything? So we stretch reason in doing philosophy or we tell stories to wonder what might lie beyond our experience.

Strictly speaking, though, atheism is just the denial that God exists. The rest is figuring out the philosophical implications and thus the atheist's best positive worldview.