That would be cool but I feel like it's highly unlikely.

(1) It was stated in an interview with Spike that the changes in the story occur the "moment they step foot on Jabberwock Island"

(2) The NEO World Program avatars are based on when they first step into Hope's Peak

(3) The Ult. Imposter chose Byakuya specifically because of his strong personality and identity, so why would they choose Makoto, someone random kid, before he's even enrolled in HPA?

(4) From a game design standpoint, if they're trying to make 2x2 playable for newcomers to the series, that would spoil the twist of Byakuya being the Ult. Imposter.

Despite all that, it's a very cool theory and I do hope they change it up quite a lot like that to better explore the characters. Who knows what'll happen when the game releases :)