I love Youjo Senki, obviously. It's hard to tell if it will go full reddit atheist, but thus far, it does not seem to. The anime, manga, and light novel are all quite different stories, more like three different authors were given a story outline and each made their own distinct stories that still hit the same general plot points. In the manga and light novel, Being X isn't some nebulous demon pretending to be God, it's the whole pantheon of gods: the Christian God, the Muslim God, the Hindu Gods, etc all working together. It's really fucking stupid, in my opinion, and is a prime example of why "less is more" has become a saying. Removing the mystery behind Being X just raises so many damned questions around what's happening, and why all these various gods who are directly opposed to one another would be so highly interested in fucking over this one dude in particular, and it remains to be seen if that will kill the story or not. At least when it's a demon pissed that it didn't get instantly worshipped, it makes a lot more sense.
Still, I sort of doubt an "enlightened by my atheism" story route given the source material, for what it's worth. Another season is coming btw.