God Break Down the Door - first single

[elevenism]

The characters could believe different things about what The Presence is than you do.

true.
Let me say this. Look at the time period of YZ. We're talking early sobriety for the artist, right? All the 12 step programs and most rehabs are based on spirituality. They CLAIM that they aren't religious, but 6 of the 12 steps mention "god" if I'm not mistaken.
I went into that shit vehemently anti Christian and got a serious fucking dose of spirituality. But there is no dogma in it. It's more of a "spirit of the universe" or " higher power. "
Still, I would argue that MOST people who go through recovery are like, for instance, praying at least at the meetings.
They do that. They have group prayer and then claim they aren't a religious organization.

So okay, this recovery works and you're told that it's the work of "god."

And I think a lot of people then start looking at the hypocrisy of organized Christianity and see a sort of disconnect there.

I REALLY think that this may have partially informed Year Zero: it's this idea that there IS a higher power, but people have it wrong (like the church of plano.)
In fact, a lot of what is claimed to be "Christian" is the DIRECT OPPOSITE of what it's really supposed to be about.

so I think there is this kind ... I think a big part of the YZ story is about THAT. It's about people being self righteous and judgemental (god given) while the ACTUAL higher power is right there and it's PISSED (the warning.)

As to the nature of the presence and whether or not it's aliens: I have no fucking idea what the physical nature of god is but it COULD be something that seems very alien. I feel pretty certain that The Warning is about SOME kind of higher power.
It's hard to find people who have been through recovery who don't have some degree of spirituality.
The few that don't came up in specifically atheist programs like Rational Recovery (Albert Ellis, based on RET,) and S.M.A.R.T., but those people are pretty fucking few and far between.

THEN, you've got the metaphor idea that @streetman mentioned. I could be TOTALLY wrong and GBDTD could just be that.