It doesn’t violate the red. It just twists it more fancifully. There’s no contradiction inherent in this nor any reason we shouldn’t think it’s possible since the “Witch Narrative” layer is doing the very same thing with the “Mystery Narrative” facts.
My point is the red can be read in multiple ways, and the speaker is under no obligation to specify which reading they’re using. Beatrice may – and does – speak in “facts related to the closed rooms specifically being discussed” and “facts in general,” sometimes switching between the two without clarifying. That’s her goal as the person trying to pass off the highest possible layer as valid and get the player to concede and accept it. There’s no reason to assume that’s the only trick up her sleeve, however.
Bear in mind that upon realizing the truth Battler has an awful lot of sympathy for someone who, if he is strictly aware of the truth as a function of the “closed room murder mystery scenarios” (or whatever you want to call each “puzzle”), is just repeatedly and meaninglessly slaughtering people. Is it not more probable that he realized the deeper truth of “Everything was intended as harmless fun, but something went wrong that was not necessarily her fault?” And if so, should we not be able to find this narrative pattern in the stories in addition to the one that lets us solve the puzzles?
And as I’ve demonstrated, the red is porous and the regular text indicative enough that we can, in fact, find this narrative, even when it runs directly counter to the puzzle scenarios.