The Voice of God explains at the end God isn't really a woman, (s)he isn't really anything. Since Loki and Bartleby likely saw God as his most vengeful, they refer to God as a He. But to the Muse, she sees God at her most loving, so she refers to God as a She.
Any being lower in the spiritual hierarchy than God can't perceive God as he/she/it actually is, therefore, each of these beings "interpret" God as something with which they're the most mentally comfortable when in his/her/its presence.
It's similar to what happens when a lesser being hears the voice of God. Also, this is why all of the female characters see a woman and all the males see a man; the similarity to themselves comforts their minds.
I have learned from experience... that a modicum of snuff can be most efficacious.
My interpretation was that Loki and Bartleby were banished so long ago, they were still used to the old testament god. When Loki considers his crusade against the Mooby people, Bartleby says something like, "there hasn't been an angel of death since you quit. don't you think god may have changed his mind on that?"
They were used to the old vengeful god known as YHWH, not the heavenly loving father Jesus speaks of. They were banished out of heaven even before Jesus was around.
So as a result, they probably refer to god in a more archaic way, "He", which is what all ancient Hebrew scripture says. Over time, god may have changed a bit, and they weren't around to see it.
This is sort of one of the themes of the movie: Loki and Bartleby are angels of a much older era, and don't fit in with the times well.
I liked the movie Prophecy (1995) where Christopher Walken as the angel Gabriel is looking for the most evil soul he can find. He says there has been an endless deadlocked war in Heaven between Angels. He is confronted by Lucifer at the end.
when the protagonist asks Walken why he doesn't just ask God if he has questions. Walken said "He stopped talking to me a long time ago". Gabriel is jealous of humans referring to them as talking monkeys because God has set them first.
He also says you would not want to meet an angel saying who do you think God sends out to do his bidding. "I can crush a baby's skull right in front of its mother without batting an eye."