That seems a bit muddy to me. I have a personal preference for a system that creates unique religions rather than a bunch of churches, each with a grab bag of deities. Especially since random behaviour over hundreds of game years will almost certainly shake them up to almost truly random with some mechanism of separation or domination.
I'm going to assume there's more than two layers, since a dwarf should be able to have a personal relationship with the deities in his religion's pantheon (patron saints, for instance). I like the idea of there being an 'official' religious position defined by the priesthood (much like a civ's position would/should/will be defined by it's 'culture' and changes heavily influenced by the rulers)
I also think you are making a mistake by preaching relativism so hard. Things should get better, because good ideas stick around where bad ones get dropped. If practices and religions don't evolve to better suit their civs, there's a problem. A religion that better suits the actors involved IS a better religion.
Admittedly, I may be biased in thinking that monotheisms developed and spread during world gen make for a better story than the history of a bunch of drunken rednecks fighting on a mountain for centuries. Blame Salvatore's Demonworld, which IMHO is the best use of religion in fantasy ever, by 3 orders of magnitude. Compare it to the FR's Avatar series (Blech)
Back to this:
What if you generate a world, where gods can literally absorb smaller gods? What if this event happens as a result of changing belief structures on the world? What if it happens regardless of people's beliefs?
How is this different from the absorbtion mechanic mentioned earlier. It seems like you are presenting multiple mechanisms for this to occur, with different ones being true for different worlds. Would this simply be a binary switch? The alternative is to create a continuous spectrum of possibilities, and I don't see that happening.
I feel very strongly that if there are too many metaphysics active in a singleworld, things stop making sense (hence the drastic split between prophet/enlightenment based mono's and active gods polys in the OP. Two sets of metaphysics only.)
I'm not saying that more shouldn't be possible, just that worldgen would need to pick a functionally complete set of metaphysics from the possibilities and turn off everything else. Unless some things are possible in some worlds and not in others, your worlds won't be a spectrum of colour, they'll just be a big splotch of indifferentiated grey.
One thing that hasn't come up is the concept of loosely associated patron gods. The god of the Babylonians versus the god of the Assyrians kind of thing. I suppose that's just a case of simple cross pantheon rivalry, but it muddies the water between belief and worship.
For added complexity, religions could also maintain an enemy list. This would be gods that were, not only disallowed entry to the pantheon, but actively opposed by the religion.
If a religion has a position on a deity, shouldn't that deity be in the religion's pantheon? By definition, if nothing else... I don't think you'd say that Satan wasn't a part of the Christian religion.
You mention:
Currently, a church dedicates itself to one god, and builds it's religion/faction around his actual spheres.
Which is similar. Greece had temples to Athene and Apollo and whatnot, but that didn't mean they were different religions. They just had different patrons. While that's an argument for creating cults and heresies within a religion*, I don't think it justifies creating a separate religion. There's more in common than there is different, so it makes a good container entity. It's kind of what I meant when I said Null-Pantheon. The problem (IMHO) isn't that temples are created to a single entity, but that there is no relationship between deities
*Interesting... Cults, Heresies, and Monastic Orders could all be handled by the same mechanism under religions... The only difference is how they were treated by the main religion. Adds a fourth layer to the entities
I think any mono-creation system should be able to support Confuscius, Buddha, Christ, and Muhammad (That is, founders with varying levels of personal divinity attached to their person's) on a continuous scale. This gets back to your variable metaphysics. In a world where these things have evident power, the power level (divinity) of these emergent godheads should be set by world. Possibly with a low std dev. as well.