I think I finally had an epiphany.
Let me see if I can work through this so that it makes sense, because, for me at least, it seems to explain why I'm having such an uphill battle trying to make my point.
The difference here is between a resource and a setting. The Planes (not Planescape, but all the Planes) are a single setting, not a resource.
Take an orc. An orc is a resource. There is no really inherent elements of an orc that I can't mold, change or eject and still have it recognisable as an orc, by and large. By default, orcs worship Gruumsh, but, if I want demon worshipping orcs, no one will bat an eye. If I want pirate demon cultist orcs, again, not a problem. Heck, if I want demon worshipping, ninja pirate orcs riding dinosaurs, I can probably get away with that and, while people might not like the idea, it won't be criticised as a canon issue. Orcs, as I said, are a resource. There is no real expectation that an orc in Greyhawk will be the same as an orc in Forgotten Realms or Eberron or Athas for that matter. And certainly no expectation that an orc in any given sourcebook or module will automatically follow orc lore set out in the default setting.
Basically, you can take an orc and do pretty much whatever you want with it and it's still an orc. It's a resource for building a setting, not part of any specific setting.
But, look at how the planes are presented in the 1e Manual of the Planes. They are not presented as a resource, they are very, very specific about what the planes are, what they look like, what things you will find there and what unique, named individuals from D&D canon you will find there. Gruumsh hangs out on Acheron. That's not a resource book, that's a setting book. And all settings are defined by their canon. That's why changes to The Planes generates such strong reactions. You are messing with a setting's canon and that setting is pretty specific and has loads of lore for it. All you have to do is look at the hugely negative reaction to the 4e Realms and you see what happens when you futz about with setting canon.
Compare the MotP to something like Sandstorm, which I would call a resource book. In Sandstorm, it defines a wasteland in broad terms, whether big or small, above ground or under, magical or not and then outlines a number of different options that you may or may not find in a given waste. Then it leaves everything up to the DM to create that waste area. But, the MotP doesn't do that. The MotP defines every plane is very specific detail.
See, my mistake was always thinking of the planes as a resource, same as you would treat the Prime Material. In the Prime, if I'm running, say, Eberron, there's no expectation that Faerun also exists in that campaign setting. It might if I add it there, but, there's certainly no expectation that that is true. But, in The Planes setting, the planes are single, unified setting. An orc in Faerun is different from an orc in Eberron. But a Yugoloth is the same in both settings because Yuguloth come from The Planes setting. My other mistake was thinking that this was a Planescape change that came in later on down the road. But, really, it's always been that way. The planes were never a resource for the DM, or at least, not for a very long time. They have always been The Planes, defined and detailed as a single campaign setting that never changes regardless of where you come from.
A character from Athas, or Ansalon, or Khorvaire or Faerun who travels to Acheron ALWAYS enters into The Planes setting. And The Planes isn't a resource where the DM is expected to create a campaign setting from the building blocks provided. It's a complete setting unto itself.
And without canon, you cannot have a setting. Settings are defined by canon. Resources don't need canon, they only need suggestions. Note, not all Prime Material monsters are resources either. Drow come to mind as something that are much more of a setting than a resource. If I feature drow in an adventure, that comes with all sorts of pretty strong expectations based on the lore surrounding Drow. I wouldn't expect to find a Drow castle aboveground, for example. Planar creatures and elements are far more like Drow than orcs or kobolds. Orcs and kobolds and the vast majority of Prime Material goodies come with suggestions - Kobolds might be slaves of dragons, or they might not be. But the planes never change. Heck, look at Remalthalis' reaction to my idea of changing Acheron. In a resource, that would be perfectly fine. But Acheron is part of a complete setting and it has canon. It cannot be changed. If I want a post apocalyptic plane, I should use a different name, because Acheron is already established as its own thing. If I wanted blink elves, I should find a new name, not repurpose an existing part of canon of a setting.
Does this make sense? Is it fair to say that The Planes are a setting and not a resource?