The kind of weirdness that "doesn't work" and people find annoying is weirdness for the sake of weirdness. Yoko Taro's weirdness usually has an underlying logic to it in the world of the game that matches all the other weird stuff in the game. His games are also mysteries largley, where the characters in the game are figuring out what is actually going on around them. This includes designing the game in such a way that the player plays through the events of the game several times over by design, but each time, the player knows more and more about what is actually going on. So yeah... Yoko Taro's game are weird. They also know they are weird and give the player time to figure out the weirdness. Most importantly, they don't feel... condescending towards the player with the weirdness.
The ending of FFVIIR feels like... weirdness for the sake of weirdness. And for a large sub-set of the players, it kinda feels condescending in a "yes, we know you want the story of the OG, but we'll literally rise above that in-game to keep it from coming about" way. Like... the weirdness doesn't feel like "genuine" weirdness. It feels "fake".
