My point is that they are just required to get to the place not because the quests have any kind of flying built in to them. Some well placed flight paths (and the most common questing hubs in that map have flight paths nearby) would work just the same way. Of course, once we are there we still use flying because flying doesn't have any downside: it's faster, avoids danger, it's cool to fly around... etc.
Everything you named points in the same direction: dismounting the player. I am more inclined to think that at this point it would be more interesting to add gameplay to the sky that doesn't revolve around dismounting. But this is more something to talk for the future.