I know the series' writing is not the best at times but it still upholds standard conventions of narrative. Throughout KH3D Lea's plot and arc is pretty straightforward and it begins with one mystery that isn't resolved, the thing that primarily drives him throughout his journey -- "Isa (and Braig) should've been recompleted like they were, so why aren't they here? Where are they? And how can I go about saving Isa?" -- this mystery is the driving force behind his story in that game and is the focus in nearly every one of his scenes. It's why he goes to Yen Sid. It's why he becomes a Keyblade wielder. The only remaining question before entering the story's endgame is where are Isa and Braig. The game then answers that in the climax, bringing his arc, at this stage, to a close. For Isa to be anyone but Isa completely defies the narrative structure of Lea's story in that game and it just doesn't make sense with what is established. By the end of the game, Lea's arc, started at the beginning of the game, is completed, allowing for his character to move onto the next stage, being saving Isa using the knowledge (where Isa is) and the abilities (Keyblade) he gained over this journey. Even though it is technically possible for Isa to be Saix due to KH lore, it's not really probable given these facts and just taking basic narrative structure into consideration.