Short answer: No, there are discrepancies that make it seem impossible for the game story and the manga adaptation to be sharing the same canon (not counting the possibility of as-of-yet unconfirmed in-game alternate timelines).
Long answer: It is easy to say “the Prefect does kendo in the manga but not in the game, so Game Prefect cannot be Yuuken,” but there is no proof in the game that Game Prefect wasn’t on their way home from kendo practice before waking up at NRC: the Game Prefect being a high school kendo-club member is technically not impossible.
So why does everyone say that the manga isn’t canon to the game? That is because of discrepancies: conflicting parts where the same exact situations are handled in two different ways, meaning that we have to choose one, because it is impossible for both to have happened.
What happened in the game is what happened in the game, and what happened in the manga is what happened in the manga. The manga are canon to themselves, but not to the game.
Examples:
One of the biggest changes in the manga is the prologue’s climactic mine-monster scene, where the prefect, Grim, Deuce and Ace all work together to successfully defeat an enemy.
In the manga, they fail: it is Riddle who defeats the monster. He takes Ace and Deuce back to Heartslabyul, leaving Yuuken and Grim to present the magestone to Crowley alone.
It is not possible for the four students to have defeated the mine monster together while Riddle simultaneously defeated it for them, it must be either game canon or manga canon (the existence of in-game alternate timelines is, as of this writing, unproven).
And this is a particularly fascinating change: Manga-Riddle even has a dismissive line about the group struggling with the monster (“Honestly, how can you let such a low-level monster give you so much trouble?”), as if monster-battling is such a common part of the world that they, as day-one first-year students, should be able to handle it, while in the game Riddle dismisses the idea of a mine monster existing at all. (“Don’t listen to them. They’re so tired, they probably just saw a wild animal and thought it was a monster.”)
Another notable change is where Ace goes to Deuce’s rescue in the game story, but in the manga adaptation there is a panel of Ace running away as Deuce fights the monster, as though to save himself.
There are many other differences in the manga, such as the prefect not reuniting with Grim until his second day at NRC instead of fighting ghosts together at Ramshackle, Yuuken having his cell phone and kendo sword while the Game Prefect lost everything, and how the destruction of the chandelier in the game never happened in the manga.
In the manga Yuuken never makes it past Main Street before he is expelled.
Crowley assigning the window-washing task, Ace running away, Deuce’s introduction and the throwing of Ace at the chandelier are all non-canon to the manga.
Similarly, the prefect waking themselves up instead of being awoken by Grim, attacking Grim with a broom on Main Street, Riddle defeating the mine monster, the prefect and Grim going back to Crowley alone instead of with Ace and Deuce, etc., are all non-canon to the game.
It is interesting how both the original game story and the manga adaptation are following the same basic premise while integrating such important story changes at the same time.
It is for this reason that the manga-based anime will also maybe not be canon to the game. And, depending on exactly how strictly the animated adaptation is to follow the manga story, the anime might also be only canon to itself rather than having any canonical relation to the game, manga or novels.
Exciting to look forward to!
Twisted Wonderland Reference Note 