The Great Wheel, at least in Planescape, is not a canonical fact, it is a canonical hypothesis by fallible characters in the setting.
Right, that's the excuse isn't it? It isn't "true" it is just what people think is true... and is the major version presented to DMs not from the perspective of scholars, but from the perspective of the game designers.
So, for example, the 23rd layer of the Abyss (The Iron Wastes) isn't REALLY the 23rd layer of the Abyss. Of course, if you talk to someone they will call it the 23rd layer of the Abyss, and if you look to official sources it is referred to as the 23rd layer of the Abyss, and if you had to find an artifact and it said it would take you to the 23rd layer of the Abyss then you would likely expect it to take you The Iron Wastes... but other than being called that, referred to as that in meta-game resources, and being listed in that order, it isn't
really the 23rd layer.
But... what is the difference?
Also, while maybe it isn't shaped like a wheel, none of the places listed as part of the Great Wheel don't exist. Bytopia exists, and the ancient oak Whisperleaf still grows in Shurrock in Bytopia. These are all true things. It isn't like Whisperleaf is secretly in Valhalla instead. So it isn't just "a canonical hypothesis" it is as good as fact because even the DM is not presented with a different set of things. Without removing Bytopia as a place that exists, there is no model that says "actually, the plane of Bytopia is really X"
The people who came up with the model are fallible. They are the game designers of Dungeons and Dragons and only human after all, but you can't present a "complete cosmology that accounts for everything" and then expect to be able to hide behind "well, this is only the best guess of mortals who can never truly know" because this is also the model we are given for the DM to run Demon Lords and Gods, who would have a far better understanding if there was something else that was true. And if it was an incomplete model, it would have pieces that were incomplete or didn't fit. Just like real-world "unified theories of everything"
Edit: Next post I was going to respond to from
@Micah Sweet covers the exact same point. It doesn't matter if you can't look at them from the outside, If the planes were all really the scales on the back of a cosmic serpent then the books need to tell us that for it to be true. But no game resource comes in and says "here is why the Great Wheel is wrong" It is always portrayed as true, except when it isn't in use.