Bianca actually says in game that by the time she made it to Striaton City Gym, the events of the castle were over. Its her fault they weren't there.
Yeah it's true that the game doesn't cover all of the things the manga does, but I do think that the fact they hinted at that in the manga, maybe says something about how things are in the game. It's because I don't see a reason to create unnecessary complexity by hinting at certain things in the manga, if it weren't for a reason.It's possible, but doubtful, due the fact that as Kaori said, it might have been hinted at even a bit. Also, while Yoshikko made a great find, the manga strays a bit from the games, and while the Shadow Triad may be revealed as the Striaton Leaders in the Manga, their identities might still be left a mystery in the 3rd game, as instances like Karen being part of Team Rocket and all that never happened in the games, but the games also never gave us reason to think that it didn't.
If the three gym leaders were really the shadow triad, there would have been a bit more hints to that within the game. That's what I would think at least.
Pokemon "Grey" should do this. I think that the Striaton trio didn't have any story with them. At the end right before you fight N and Ghetsis they challenge you to a triple battle. 3 Stoutland, Simisage, Simisear, and Simpour vs your team.