There's the book The Last Church along with lore around the Emperor's rise to power.

During the Unification Wars, the God-Emperor (although he wasn't called that at the time) exterminated all religions because "they held back humanity" since he must have spent too much time on the atheism subreddit while he lived in hiding. This is funny because religion had lasted all the way through the Golden Age of Technology that saw humanity conquer most of the galaxy and fulfill everything the Imperium supposedly stood for.

Then in an even funnier twist of fate, the God-Emperor gets his shit pushed in by the demonic forces of Chaos after the corruption of his favorite son and many of his forces. If only he was smart enough to realize the religions he exterminated had been honing the art of resisting everything Chaos stands for (Pride, Lust, Wrath, Disease, Hatred). His "atheist rationalism" was conquered by the supernatural, his pride condemned him to the Golden Throne to be worshipped as a god himself, and humanity was doomed to millennia of slow and painful decline.

It was the classic neckbeard hubris of declaring oneself to be an enlightened genius because of atheism while actually being some dork on a web forum.