It sounds like you generally wouldn't be able to skip at all, then, because I doubt many players who have gone through a part of the story would have a great incentive to repeat a boss or dungeon unless they're helping a friend to clear it. And there are those players who have a habit of only ever seeing the cutscene in the inn. They will want to skip even the first time.

Honestly, I don't see this as an issue that should be fixed with programming. It's more of a community / player culture issue, and the simple resolution is for people to just live with how other people approach the cutscenes. The only time it actually becomes a game mechanics issue is if combat autoinitiates on cutscene end.