I'm going to warn you now, this really is a long-winded, rambling bit of nonsense regarding D&D cosmology, creation myth, and all of that silliness. Read at your own risk.
The kind folks at Wizards put in a few different cosmological models for every DM to choose from with this most recent edition. We have the classic Great Wheel (my personal favorite), the tree one (that I'm not that familiar with), and the Astral Sea and Primal Chaos (which I guess was introduced in 4e?). I've recently spent a little too much time reading the various articles and what have you about the nature of the D&D multiverse and it made my eyes cross.
Now, the easy way to handle it is to say "Screw it. Oerth exists and Toril is someone's fever dream." Or vice versa. There are no other worlds, etc, etc. I grew up reading DC Comics, so as a result I can't do that. The thing is, the different "In the beginning" stories for each setting don't really mesh all that well together at times. We have Tharizdun trying to destroy everything in Oerth's distant past, Primordials looking at the Prime Material Plane and yelling "Gimme!" over in the Abeir-Toril neighborhood, and who knows what else. I'm not that familiar with many of those apparently awesome settings that came out in the 90s and possibly later. I mean, warforged! How awesome are they?
Now, keep in mind, I'm just rambling here. This is how I've decided to reconcile all of this craziness so that if, for some insane reason, I want people from the Forgotten Realms to visit the World of Greyhawk or vice versa, it all make sense. To me, at least. And honestly, it probably won't ever even factor into the game, but damn it, DC Comics!
So this is my thought: in the beginning there were primordial gods who did stuff. Exactly what kind of stuff? Who knows for sure. These gods predate any and just about all of the current gods running around out there messing with mortal lives. And, for whatever reason, most if not possibly all of these primordial gods, who didn't require the worship of mortals because there weren't any, are dead. Or whatever passes for dead for a supposedly immortal being. Thus we have giant, petrified dead gods floating around the Astral Plane with Githyanki cities built on them. Tharizdun may have been one of these gods, as might have been Ao. Atropus was probably one of them, but now he's just (just!) a petrified undead head travelling around the multiverse stamping out mortal life wherever he (it?) finds it. If Asmodeus is, in fact, Ahriman, then he would be one too. But of course Asmodeus is a big, fat liar who spreads so many stories about his past, who can know for sure which version of his origin is true. Jazirian, the couatl deity, may also be part of that most ancient group of gods.
So, from nothing, or the Primal Chaos, or who really knows, the primordial gods appeared. They, in turn, began the shaping of all things, and from them came the oldest gods. It's arguable who these oldest gods may be, but this is a creation myth, so different names get tossed about depending on who is telling the story. They, in turn, gave rise to still other gods. And somewhere in all of this, the Prime Material Plane came into existence, and mortals started popping up like dandelions. So this is my thought: originally there was only one world. Somewhere along the way, something happened. Something truly cataclysmic. Maybe is was Tharizdun's attempt to destroy all of creation. Maybe it was the Primordials getting grabby. Whatever it was, it happened so long ago that only some of the most ancient beings in the planes know exactly what happened.
Anyway, this cosmic event caused the Prime Material Plane to splinter. What was once one was now many, and this is why so many different worlds resemble each other so much, with many having many of the same races. There are variations here and there, of course: Krynn doesn't have orcs and has kender instead of halflings, Eberron has the warforged, Athas has scary cannibal halflings, etc, etc. Separated, each world began developing in its own way. Btw, I'm not sure how I feel about this Crystal Sphere thing that Spelljammer has going on.
Now there are all these different worlds. Prime real estate for the molding. And wouldn't you know it, there are a gaggle of gods wanting to do just that. So there is a great, big cosmic landgrab and once those lucky gods and goddesses get in there, they start up their mythological PR machines, getting people to believe in their version of how it all started. Of course, some of those gods know more about those early days than others. Some of the youngsters probably don't really know that much more about it than the mortals do. And those who really know are either not talking, making up stories, or are dead and gone. The few remaining obyriths probably know the real deal. Ao, maybe Asmodeus, the oldest of the tanar'ri such as Demogorgon. Regardless, the truth of the matter is buried under so much conjecture, divine spin doctoring, and misinformation that very few know the real story. Then mortals start travelling the planes and sharing the stories of their own world with people from other places, and myths start getting combined and it all becomes a big mess that religious scholars and planar sages spend all their time debating. And of all the races populating the various worlds of the Prime Material Plane, only the aboleth really know what is going on, but they don't care to actually share this information with anyone else.
And just to mess everything up even further, along come the illithids, conquering world after world and threatening everything. And no one knows where they came from, not even the aboleth. Fortunately, events and their own arrogance conspired against these brain-sucking monsters and Gith and her followers destroyed the Mind Flayer empire and nearly exterminated the race. However, groups still exist here and there, which is why some worlds have them and some don't. And some worlds, like Golarion (that's right, I said it), once had mind flayers but were pretty much wiped out. However, some remnant still remains in the depths of Golarion's Darklands, the neothelids. Because as we all know, a neothelid comes from an illithid tadpole that didn't undergo ceremorphosis and wasn't eliminated by a colony's elder brain because it was dead. Sounds like the work of githyanki to me. And if the mind flayers are dead, and they either don't know about or care about the neothelids, then the githyanki have no reason to return to Golarion anytime soon.
And we all know that the Whispering Tyrant is a mystical echo of Vecna brought about by the Maimed God's attempt to recreate all of reality in his own image when he invaded Sigil. Right?