But you ignore the other side of the paradox, as I state it in the article. Naturalizing the unnatural misses the Kantian or mystical point that some things might be inherently beyond our comprehension. But by the same token, appealing to that mystery as an explanation is empty, and personalizing that mystery is another form of naturalization. So positing this mystery is consistent with atheism.
As I say in the article, "Conversely, if you were positing something supernatural, how could you be explaining anything, as opposed to telling a tall tale?"
If something's beyond our comprehension, such as the origin of all that can be naturally explained, then no one knows what they're talking when they talk about that origin. That would amount to agnosticism plus doubt about any pretender myth that's supposed to bypass that unknowability.
You speak, for example, about a possible "reason" or "cause" of nature, but those are naturalistic terms. To say that God is the supernatural cause of the universe is to speak oxymoronically. If God is supernatural, he's no cause at all. If God's mind is beyond ours, we can't speak sensibly of his "reasons." God would be beyond good and evil, and beyond reason and irrationality.
That's the other side of the coin.
I'm assuming methodological naturalism here, not the metaphysical kind.