I strongly disagree. Cosmology is a setting-level decision, not a game-level decision. D&D has always been a game that encompasses a multitude of settings, and arguing that cosmology is an inherent part of the game and not of any given setting is disingenuous.
Eberron has its own "orrery" cosmology. If you're making a setting that centers a Norse-like culture, it makes sense to have a cosmology based on the Nine Worlds and the World Tree. Primeval Thule doesn't have other planes – summoned creatures and the like come from other planets instead. 4e/Nenthir Vale had its own take on cosmology with a far more chaotic bent, with various domains spread out across the Astral Sea without any particular order to them.
There's also the issue that the Great Wheel cosmology is bad, and the less use it gets the better. Sigil is cool, but the rest of it is just box-checking (except for the part that's ripped off from Dante's self-insert fanfic).
First, I want to distinguish between a setting that is a D&D setting and one that uses the D&D rules. A D&D setting is a setting designed by the owners of D&D (TSR or WotC) for the D&D game. That excludes third party settings (Primeval Thule), guest settings (Exandria, Kalamar) and settings converted to D&D from other media (Middle Earth, Rokugan, Magic the Gathering). Yes, that is a very small list by intention. This is not to say these settings are lesser (some are quite good). Just that the D&D settings designed for D&D should have a common set of assumptions:
* They aim to support the vast majority of the D&D core rules of the edition it's currently being produced for. That means setting assumptions will change when the rules update. (Why are there sorcerers on Krynn? Because they are in the 5e PHB). O
* They support the general assumptions of the game, except when used to differentiate it. For example, Dark Sun uses an antagonistic view of magic as a key selling point to the setting and reinforces the themes. Making spellcasting harder is not a key component of Spelljammer, so the choice to remove complications arising from jamming was a good one; it didn't add as much value as it did add headache.
* The are mechanically compatible. A monster, spell, or subclass from one setting shouldn't be more powerful because it's designed for a specific setting. A DM, if willing, should be able to mix and match options and not worry about various power levels being incompatible.
* It should connect to the wider Multiverse. The D&D game has some unique IP that only D&D gets to use, it should use it. Named wizard spells, unique artifacts, mind flayers and beholders, etc. A setting should still feel like D&D, just with a particular set of wallpaper on it.
This is what should make a D&D setting unique from a setting like Golarion or Tal'dorei. It should embrace the fact it's not some 3pp setting tiptoeing around IP, it should embrace that lineage. And yes that means some compromises (such as Eberron's cosmology being a cosmology within a bubble in the wider Great Wheel, or the First World echoes explaining Tiamat and Tahkisis). Make the settings link. Let kender wander through portals to Faerun, dhampirs lurk on Krynn, and Spelljammer vessels call port in Eberronspace. Let the Mists pull people from every setting and Planescape factions swell the ranks with the clueless from every world. It's the one thing that separates them from any setting you or I can put on RPGNow. Let them use it.