But nothing of that makes the theory crumble at all. Yes its focused on Riku and Sora but honestly they are not just telling stuff that arent in the game, they use the japanese version (which does not take away Rikus part in saving Sora in the final world unlike the english version...) to point out the theme. Also at no point did I get the feeling that they are using it to hate on Kairi. They just see her role different. And her end is still open, since they are pointing out that they have no clue where her heart is thus the speculation that she paid the price for them to jump worldlines. That does not mean that Sora cant truly save her later. Yet even if he does not, why should Kairi be an exception of dieing?
I mean do you not find it silly that Nomura gave Kairi a keyblade and left her with her PoH power for her to be mostly useless in the fight itself and then killed of for motivation? Heck who knows, maybe she has also somehow turned herself into a spirit and will have a bigger role to play in later games with that. Maybe this is even better for her character than simply being just killed of, because at least in the theory she seemingly was the one that helped them escape the worldline or at least was the one that paid the price. If it was not some passive wishing again, then that sounds at least like some more active role to me.
The thing is, this theory uses examples from the game to explain their theory. And it should be viewed as that and not true the eyes of "oh my god they are shippers, thus they must have done this to destroy character x or ship y". Look at the overall theory and tell me where exactly they hate on Kairi? Where exactly its nothing but shipping for Sora and Riku. And where the theory itself crumbles apart and not just because you dislike that they are shippers.
Also Sora is lost. Him changing the fate of the universe (no matter if that was in the RoL or RoS) sealed his own fate. It was not Kairi at the end (as far as we can tell) that killed him, it was his act of changing the fate of all people and he seemingly just had some time left before he disappeared that he used to either save Kairi and/or see her one last time. Because YX already told him that he has misused it too much before Kairi was even killed, so her really not being saved or with them at the end does not change his fate at all. So of course even in that theory the card that Luxord gave him will help. So still not seeing how that is against it?
Her not being with them would also give Sora the chance to grow as a character and would fit with the theme of the last two disney worlds, where the characters had to accept the death or loss of people they love. While right now Sora still would have won completely only at the loss of himself.
They might bloat their theory a bit too much with details but the ending is strange. Sora and Kairi not sitting on the tree until the very end, everyone standing in a position where they are not looking at the tree but something else (which seemingly was big enough to get everyones attention) The sky being different colors in a scene that should happen at the same time. If we never had DDD thus knew that different time and things like that are clues, then maybe we could say that its an error. But having so many strange things in one ending? So many mistakes? Again we are talking about Nomura who has already said that even simply gestures can mean things.
So in the end I still dont see any good reason why this theory would outright crumble. And no the authors being shippers is not a good reason at all.
Anyway it is of course still just a theory and they are not going around stating it as facts. And of course this can all be wrong. But maybe some or most of it are right. At least right now there is nothing major that destroys it.