Yeah I think it's fair to say the Jays will be at a disadvantage come playoff time with Schneider managing, but they are still a really good team, so even with Schneider costing the team games here and there with bad bullpen management or whatever, they should still be 90+ wins by the end of the season. If the Rays end up being 100+ wins, then there's not much you can do about that.
The 2021 Jays missed the playoffs by 1 game, and Montoyo literally punted a game on purpose just to teach Tyler f'n Chatwood a lesson. I don't think the Jays have to worry about that with Schneider, at least I hope not, but regardless, the Jays seem to have a type with managers so it's not like they'd replace Schneider with a vetrin. It will be another yes man who will do what the org wants, and most orgs do that now. Even Boone is a puppet for the Yankees front office. Cash is as well, except the Rays as a whole are very smart, so it doesn't come off that way.