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One thing about my system is that you can incorporate manifest zones and bleed over effects for when these planes drift close to the material plane. However, since it is not based on set mathmatical orbits, and more like ships floating in ocean currents, its impossible to predict exactly when a certain plane will move close to the material. Or even when two planes might "bump" into one another, causing all sorts of havok. It does make a certain amount of sense, the unpredictability of it, since the planes themselves would have been just as damaged as Earth was when the planar reintigration occured.

For cosmology, what would probably be the best topic to discuss next would be religion. Not who the deities are or what they do, but rather how the people that worship them do so. Let's pick one deity, and start from there.

Well, I find the most interesting settings are created when the dieties prefer not to get deeply and obviously involved in mortal affairs. Perhaps they would get involved, but they have some sort of pact with each other to avoid getting involved, so that they don't inadvertently destroy the mortal world. That way, their miracles must either be done through clerics, or subtlely enough that the other dieties don't notice.

Yes, but modern, real-world religions are different enough from most fantasy religions that no comparison is really possible.

Can't we just leave it unstated and open to interpretation?

For an "official" answer, I would say polytheism, where each named diety represents a certain force that may appeal to each individual.

What I would do on top of that, however, is provide multiple possible interpretations of the nature of those dieties. For example:

#1: They are actual "gods" of their respective pantheons.
#2: They are all the same higher power, and the various titles only signify one of the power's many active roles.
#3: They are not gods, per say, but rather are powerful spirits / demons / entities that inspire reverence.

Following a traditional D&D cosmology tends to lead to one of two things (or in D&D's case, both): Overcomplication, and overexaggeration. Last I checked, D&D had a list of dieties bigger than my phone book and a description of each afterlife that included "impossibly" in every other sentence. This should really be avoided if at all possible, and the easiest way to do that, in all honesty, would be to just keep the higher powers just as much off limits to the readers as they are to the characters. Might make it seem like a much more believable cosmology to do it that way too.