I don't really get why this is a problem in the first place, to be honest (quoting you because your phrasing was an easy jumping off point for my post, but this is obviously directed at OP as well, and anyone who is bothered by this). LOTS of things in this game - in nearly all games - make zero sense in terms of lore or in-universe consistency. The segregation between gameplay and story to allow for things that serve ONLY the former even if they "break" the latter is a concept as old as videogames. See also: When it's noon in Eorzea, it's ALSO noon in Othard! And even in Norvrandt! This, obviously, is nonsense. But it's a conceit to serve the "game" side of things.
Yeah, the lore for teleport fees IS a bit shaky, but to me it feels like it's shaky because they knew it wasn't going to be convincing, so they didn't spend a lot of time or energy trying to make it so. It feels cheeky. Like the game is going "wink wink, nudge nudge" while providing this flimsy lore "explanation", because the devs and writers know that WE know that the REAL reason is, again, to serve the "game" side of things (in this case, to provide a gil sink - yes it's a small gil sink, but as someone else pointed out, it can add up bit by bit.)