Since the Whispers don’t interfere during Intermission, then doesn’t that mean that the events also took place during the original continuity? The Whispers only appear if you try to enter the bar.
Well.... Zack is alive by the end of INTERMission, which should be impossible following the original timeline. I believe it's safe to say INTERMission happens after Sefiros and the Whispers or whatever have already messed up time and the whole story more than it was before. That's why there's no "conflict", so to say.