I said they weren't actually playing the game

They are playing the game. Just not the way you think they should be playing it for an any% run.

Technically, the only "legitimate" versions of the game are on console (n64, gc, 3ds Ique)) so does that mean playing an obviously modded computer version doesn't count?

Not if you want to hold a record. Playing a modded computer version would eliminate all boundaries and you would be able to beat any game instantly.

Like I said above there are technically only 4 legitimate versions of the game

Did I ever say that wasn't the case? Those are the versions that are being played.

the glitches were not intentionally designed for the player to use as they please as in other games.

Well, duh, they're glitches. But, again, the point of any% runs are to beat the game as fast as possible. As long as you're playing the game, which glitches are a part of, you can do anything.

Cheating is cheating no matter how hard you have to work at it. Games have rules and boundaries built in. By using glitches the player has the option of completely dismissing those rules which imo makes it cheating. Simple as that.

Cheating is morally wrong in multiplayer games, whether that's football or an fps. In a single player game, why does cheating matter? Who gives a damn what the developer intended? Games have rules and boundaries built in, which can be broken in very interesting ways without even modding to finish them as fast as possible. Who gives a shit if it's cheating or not? No one is being affected by it since it's a single player game. If you don't like the category, look elsewhere and move on with your life. But to try and be like "oh, that category that you like playing isn't really playing the game and you aren't really beating it because you're cheating" is silly.

It would be like me going up to a group of people playing basketball and being like, "You guys aren't really playing basketball because you guys are using all these made up rules. Basketball isn't meant to be played like that! Psh, come back to me when you start playing by the official rules."

Like, who cares? Just let them play.