Takes just as long as before honestly. When one ship leaves the other one almost immediately shows up.
It is however quite annoying hat they use the same ship model for both, at least in the case of the Alliance. The names are obviously different, and you see a Dracthyr on the Dragon Isles ship so it's not difficult to tell, but would have preferred two different ships being used, so it's obvious at a glance which ship is currently docked.