You didn't actually go talk to the NPC who met you when you first went to the aetheryte at L1, did you? >_>
In a narrative sense, gil is actually spent as... Toll.
Literally, every aetheryte camp needs money not just for maitenance, but also because setting up an aetheryte camp is very costly and most of them had to be repaired/salvaged after the calamity, so they are deep in debt with ul'dahn investors, and excerting a toll from everyone who uses their aetheryte as a gate (paying on exit since you can enter anywhere but exit on a gate) is a way they use to pay back their debt.

It's explained by an NPC at level 1 if you remembered to talk to him! He even mentions the true physical cost of teleporting, which is an energy known as anima, yet the cost on the body is so minimal that it doesn't really matters how much you have or how much you spend.