Exactly, it's why I start this thread.
The solution could be either game mechanics or lore. Though, I'm leaning more towards lore.
First, let's look at time itself.
When there's a persistent or passage of a game time, it could be tied into time management task.
Meaning, there's only so much you could do in the day before the day is over. Though, I haven't playing any mmorpg that made me truly feel that I had to management my game time.
As for the passage of time, you could perceived it in two ways, unless if it can be extrapolated from the lore in reference to Earth time.
Time could either be literally moving at the same pace to the perspective of the player, or at a different pace.
This means, if you were able to throw an Earth watch into Eorzea's realm, it could either tick at the same pace, or a different pace.
If it is the same pace as time on Earth then it'll be easier to accept how adventurers aren't getting fatigued from long battles, because the passage of time is the same.
The day night cycle on the other hand deals with something else, or at least as we assume it is still planetary rotation and not something else entirely different.
Day night cycle inherently is used to measure time, but in no sense is it time itself.
All we know is that they measure time by looking at the sun and moon with the book of the Five Ages.
Also, correct me if I'm wrong here, but the passage from Astral Era to Umbral Era does not seem like it's based on any fixed amount of time like a century or millennia would, but instead is an era that is distinguished by an event.
One of those event being what occurs during the main story line.
As I've mentioned before, to keep passage of time consistent in single player games, the game can adjust the time to appear correctly to the time progressed.
If this was applied to mmorpgs, which it isn't, there could be a multitude of other issues to deal with.
-game events scheduled to the game time
-players perceiving the world in different lens
-time consistency throughout the world
Obviously, the other game mechanic being more natural means of transportation is not player friendly. Since no one wants to wait idly while something mundane occurs.
While those idle moments can be filled in with other activities in between, it doesn't have the same appeal as instant/faster transportation.
With each addition of faster transportation, it should make the world feel smaller. Lore could play a role in explaining new means of transportation technology.
Weren't Biggs and Wedge also trying to build better airships as well? Couldn't they somehow weave it in anywhere without it being too convoluted?
It's easy to laugh it off as just another small blemish, but would be more impressive if they've acknowledged it.