The portals themselves are the canon ways to travel the LEGO "multiverse", so even if characters from different IPs but the same universe can't access each other's portals was solely a gameplay mechanic, the portals' existences are not. They made an entire story pack for the LEGO Batman Movie, which could've been accessible with LEGO Movie Batman in the LEGO Movie dimension but they made the decision to not do that, because it's easier to have them as separate dimensions - since they're separate IPs (like the bonus levels suggest - which do have cutscenes and an actual story to them, they aren't purely for gameplay)