Hiya!
In a nutshell...any/all of my AD&D/D&D (re: 1e through 5e) games use the Great Wheel as a base. I find absolutely nothing wrong or contradictory with having any other campaign world, with it's own creation, it's own elemental planes, it's own, well anything and everything.
This is why:
Q1, specifically The Demonweb. The reason that had such a profound "Ah-Ha!" moment for me was because in the Demonweb there are doors to other worlds. Not "large demi-planes"... WORLDS...like campaign settings. All located in the infinity of the Prime Material Plane. Like all other planes, it's infinite. So, it is, to me, obvious that all sorts of different "realities" would be possible here.
It is easy enough to just say "Yeah, you can't get to Darksun from anywhere because not even the gods can"...and that's ok. Why? Infinity. The gods in AD&D are VERY powerful...but not omnipotent or omniscient...not matter what they tell you.

The ONLY one who is this, is the DM.
So...who's to say that in the infinite void of the PMP, waaay off at "location Infinity +3,482" there exists a whole other contained 'cosmology'? Say... Aebyrnis? (Birthright Campaign, Cerlia is the campaign 'continent') It's history of gods, how it was created, how it all works, the Shadow World is specific to Birthright...but it does tell the DM to come up with their own 'actual' creation myth as the one presented in the setting is what "clerics are lead to believe at this point". ...and...oddly enough...this is just how the world works.
How does this jive in the Great Wheel? Easy: The DM says so. I know it's cliché and seems like a cop out, but the DM is the ONLY "omnipotent god" (so to say) of any D&D campaign world. Period. Not even the designers of the game can over-ride the DM in his/her own campaign.
So...having all these different "cosmologies" all fit perfectly fine within the Great Wheel. The PMP handles much of the heavy lifting, but...just like it, ALL the other Planes are
also infinite...so, in a nutshell, 'anything's possible'.
For example, I play in a Calandia (Citystate of the Invincible Overlord) campaign. In it, the DM has decided to use the Demons/Sentinels, Arch-Magics, and To Hell and Back boxed sets. If you aren't familiar, the cosmology if those boxed sets is VERY different from that presented in the MM's and DMG. But... we still use the core AD&D 1e rules (even though it's... "For use with..." and not an official AD&D product). How do we merge them? Easy... Asmodeus, Zeus, Amaterasu, Fraz-Urb-Luu, Graz'zt...probaly exist, sure, but they are NEVER going to be able to find or show up in Calandia or it's "cosmology of planes, deities, demi-planes, etc". Unless the DM wants them to.
Bottom Line: The Great Wheel fits the D&D "Campaign Structure" perfectly. Almost like it was made to allow DM's to run any sort of fantasy campaign setting they want...each with their own rules, gods, planes, magic system, etc.
Of course, if you take EVERYTHING as literal...then nothing works. For any campaign. Even the ones that supposedly have "completely different cosmologies"; because they are still using AD&D/D&D rules...which have built-in assumptions...like "Clerics get their spells from gods" and "Magic spells are forgotten once cast". The second you say "Yeah, but in MY campaign, I'm using a spell-point system"...well, you might as well also just say "Yeah, but in MY campaign, there is only three gods; Good, Neutral and Evil and they were aspects of a single god who exploded itself on purpose...that explosion caused the formation of reality as we know it". But you still are "playing D&D"...in both instances.
^_^
Paul L. Ming