Sakaguchi-san cannot decide what is canonical and not to Final Fantasy. He is an incredibly brilliant person to be respected for what he did but that's it. Own the brand, own the rights. That is like saying there are no 700+ Pokémon because they were not made by Satoshi Tajiri or there is no Star Wars VII because it was not made by George Lucas or there is no Dragon Ball Super because half of it was not made by Akira Toriyama ... well, forget the last one. Dragon Ball has no real canonicity. But you get what I mean.
And if we really get technical, Neo-X-Death is not less than the Dark Cloud. It is the true form of X-Death, the soul fusion that possessed the tree but the force that controls this body at that time is the void itself that has absorbed X-Death.
I do not know why the question if Hyne exists plays an actual role for this. The stories about him exist and that is enough and that we know what the entirety of all sorceress power would mean, is also enough. The next questionable thing would be how much of a villain the Dark Cloud can even be called because just being a destructive force does not make someone a villain. The consequences are bad for us but that is not the same.