Also, how do we reconcile materialism and the militant atheism that’s been part of the foundation of ML parties with atheism being a bourgeois invention to flatten people into soulless automata?

Because it’s not. Every single person at birth is atheist, you have to convince people to believe it. There’s no evidence of a “soul”.

I’ve seen the downright miraculous transformations people have when they re-establish their relationship with God. It’s indisputable proof that God exists

Unfortunately, this is exactly how all religion spreads: through testimony, not evidence. “I prayed and god did this thing for me/I felt better/felt his holy presence”, people go through these “miraculous transformations”, and that automatically means god exists, because I felt a thing and I read a book that said a thing.

Why should anyone treat the material as primary, let alone all that exists?

Because there’s no evidence for it otherwise.

Yet, as far as I can tell, this is incompatible with Marxism-Leninism.

That’s because it is. It’s just idealism, with no basis in reality and MLs work in material reality. I don’t understand people who try and shoehorn religion into MLism, it’s just cope. I guess you can fit anything into religion if you ignore all the parts about god being a genocidal monster, controlling women, etc. but at that point why even bother with it anymore? Again, just cope.

only a fool says in his heart there is no God.

I’d say a fool is one who is ready and willing to believe in unfalsifiable claims with insufficient evidence.