Over the course of some quests, the player will sometimes enter an area or have the area they were in rendered inescapable until they progress further into the quest. This would naturally conflict with any mods that allow the player to leave those areas in ways the developers did not intend, as doing so would probably break the quest involved, possibly rendering it incompletable.
So, in the interest of avoiding such a conflict, I'm wondering if there's something that is common to all of those areas/quests which can be detected by scripts. From what I remember, some or possibly all of those areas prevent your followers from coming in with you, so that's a possibility. Does anybody have a better idea?