You can look at it differently. Reaching the end via a major skip glitch is primarily demonstrating the glitch itself, and the fact that it can be used to speed you up. It doesn't matter if you call
that any%, or you call any% the fastest run that avoids that technique.
I think the common rules about "any%" meaning no restrictions on glitches haven't served our categorization approaches too well. We only happen to accept such any% for Vault. For Moons we accept both "glitched fastest game completion" and "fastest game completion without major skip glitches".
The latter demonstrates how you reach the goal of beating the game, the former demonstrates how you can glitch the game into thinking it's been beaten.
But for all other categories, we can't equally accept 2 versions of each branch:
- "pacifist, warp glitch" and just "pacifist"
- "all items, arbitrary code execution" and just "all items"
- "maximum kills, game end glitch" and just "maximum kills"
It doesn't (and shouldn't) work like this. We prefer the ones that more faithfully achieve the primary goals. We also want to avoid redundancy, avoid meaningless publications. And finally, we want to only publish branches with solidly defined goals.