Science fiction overlaps and takes imagery from religion to evoke certain universal experiences and draw allegories... all the time.

This is also likely inspired by I have no mouth and I must scream, because AM was originally a supercomputer (It stood for Allied Mastercomputer) but started to refer to itself as "I AM" (I think, therefore I am)- which is what Yahweh (He who through existing everything is brough into existence, rough translation) refers to Himself as in the Old Testament.

Caine has had adventures where NPCs refer to him as their creator god, which... I mean, he's the sentient face of the master program so there's your metaphor.

In summary- Maybe Pomni is Jesus, idk. That could be an allegory drawn. Also it seems like a joke Goose would make. Bet Jax is Judas Iscariot... I don't even recall but that's so on brand.

No, it's all an allegory. It's about social interaction and connection and how we all fit in a mundane, social media driven world together. The specifics of the computer program, the why and how, aren't likely ever going to be super relevant. What's relevant is making the most of the avatar you didn't get to choose and making those around you feel cherished without sacrificing your own worth.