I haven't found any huge reason to have flying on the maps once the MSQ takes you away from them.

I have them on my main and I've got an alt that's only gotten a few of them and I've not been terribly inconvenienced by not having flying unlocked on those maps. And my alt has completed all currently released MSQ and is waiting for Endwalker to release.

The only map where it would be an issue is one they give you simply for completing the MSQ - no side quests or aether currents.