To be fair, I've had a player like that. :/ Specifically, he wanted to be a Githzerai Xaositect in a prime-only Eberron war campaign. When that didn't fly, he wanted one of his character goals to be "Get to Sigil", despite that I told him it didn't exist in my proposed game and, even if it did, his PC'd have no way to know about it. That's the problem with using PSish lore or Spelljammer stuff (or PoLand too, yes) in the mainline core stuff - it sets up expectations in a small but vocal subset of the player base.
As Weather Report said, that's a problem player, not a problem with the setting. That "small but vocal" subset you mentioned are the players who have problems with their expectations not being catered to. Removing cross-setting continuity isn't going to make those people go away, it just means they'll be irritating in another regard.
Returning to the Dark Sun examples, why did any Dark Sun stuff have to mention crystal spheres, or planes beyond Elemental planes, the Gray, and the Black? Spelljammer and Planescape, respectively, could've handled all of that, keeping it contained to the meta-settings.
Presumably because the Dark Sun fans who want to add a dash of planar material to their DS campaign shouldn't have to look through/purchase another setting's products to get their own setting's cosmological information? As it is, we're not talking about a huge swath of material here; notwithstanding planar Dark Sun adventures like
Black Spine, the material I was referencing were two sidebars in one book, and maybe another one in
Dragon Kings. That's hardly enough to wreck anyone's game.
EDIT: As it is, Dark Sun is a pretty good example of how you can have your cake and eat it too, where your suggestion is concerned.
Spelljammer's
Complete Spacefarer's Handbook gives a paragraph on Athas from that setting's point of view, and that's it. Planescape's
Planewalker's Handbook has one paragraph about Athas from that setting's point of view, and that's it. Dark Sun's
Defilers & Preservers has two sidebars on planar travel and spelljamming, and that's it. Everybody wins.
True, there were some other crossovers, but they tended to be limited to specific NPCs, items, and similar things. The general "rules" about how such things worked (or didn't work, where spelljamming was concerned) were very small and unobstrusive.
