Well, Ok' Zundu actually does have at least a logical explanation for taking gil fees for teleportation there - they actively trade with the Ishgardian knights at Camp Cloudtop, so a supply of gil would be useful for that. The aetherytes at Mourn, Zenith and Moghome are a little more vague though, although again the dragons and moogles respectively may just take gil payments in a more symbolic way (as a mark of respect, that those using it give gil to them as an offering, not a tax).

The chocoporter in those areas indeed seems to suggest the payment is more symbolic - it's not even an npc but a large chocobo statue that acts as a giant ocarina (the character presumably blows through it to call the chocobo), and the text message mentions that "it's best to leave some gil as payment, just in case..." (paraphrased). So maybe it is just a symbolic payment, a teleportation 'honour-system' if you will?

The moogles at Moghome however do end up making relations during HW's story with both Gridania and the moogles of the Black Shroud, as well as Ishgard, so again maybe they start collecting teleport fees on their behalf after that point (remember there are moogles running stores in both Moghome and Ashah, so they clearly know the value of gil and use it for something.).

Even the aetheryte at Helix in Azys Lla, an area that has been uninhabited by anything other than robots for millennia deducts payment in gil when you teleport there, and again, that sort of has an explanation in that the aetheryte, like the nodes in Helix which act as vendors and repair services, may be programmed to automatically collect whatever currency the person has (unless gil has been a universal currency since the Allag's day).

But I admit that is all a bit of a stretch....