Do I sense hostility? Or am I just imagining it.
I'm not suggesting that they should 'force' people to experience the time elapsed naturally, but that is one way of experiencing a passage of time.
If it were a single player game, they could have actually adjusted the game time to match the time actually consumed during the travel, but that can't be done here.
I wonder if there is a better way to address it with lore, rather than just chalking it up as a "Simpsons Bubble".
As Anonymoose pointed out, there's two experiences occurring side by side. The one you're having with other players, and the one you're experiencing alone.
However, since it is a shared persistent world, you can't possibility have everyone in their own time bubbles when there is an actual shared persistent game clock ticking.
When the passage of time doesn't seem to match up with what is occurring in the game according to the mechanics of its universe, it might become a bit jarring. Which is why teleportation is a fantastic way of explaining that gaping hole, and why I was wondering if there was some lore to change the way ferries and airships worked.
It's really a problem that comes mainly when the game world has an actual clock to go by. While games without defined passage of time, would have the player fill in the gaps with their own imagination.
The main story experiences is slightly different matter though, since it's more of shifting the story interpretation as the player is always the hero of the story, while other players are the hero's companions. The point of view only needs to shift. For assisting players that are re-encountering main story fights, it could be retold as reliving the experiencing again. As you can't skip ahead in the story, but can always go back to previous accomplished ones.
Though, I don't know how the game handle new players who didn't experience the calamity.
I just thought it was something interesting to think about, rather than just dismiss as player usability.