Why we pay for aetherythes

[Enkidoh]

My thoughts, exactly. Up until recently (game time-line wise), Moogles in Churning Mists never dealt with the outside world and just focused on repairing/ maintaining Hraesvalgr's domain as part of their covenant with him. Things have changed once Ishgardians have set foot there and are now helping Moogles rebuild.

Anyx Trine ... there's really no reason other than maybe they like how gil look (shiny)?

Except the group that set foot there was not entirely Ishgardian after all, only Ysayle and Estinein were. There was a Sharalyan youth (Alphinaud), a person of unknown origin/homeland (the Warrior of Light/the player), and three Gridanians (Kan-E-Senna and her Serpentguard), not including a Twelveswood moogle (Kuplo-Kop). So therefore given the fact that it was technically Gridania who made direct contact with the moogles of Moghome and not Ishgard, it could be kind of handwaved away that before she returned to Gridania Kan-E established some kind of permanent diplomatic tie between the two nations, which would explain the fees paid to the moogles for using the local aetheryte. But maybe I'm just grabbing at straws here.

Anyx Trine's one could also be explained away by hunters from Tailfeather collecting the tolls... but given the dragons who inhabit the place seem to be understandably wary of spoken intruding into their sanctuary, that's a real stretch.

Finally payment for the Azys Lla aetheryte fees could have a mundane explanation which has ironically nothing to do with Allag - as soon as you first arrive in Azys Lla, Cid explains that he has immediately set up an Ironworks airship route back to Ishgard (symbolized by an Ironworks standard at the end of the dock in Helix) in case you "need to return quickly for supplies" - taking that further whose to say he hasn't stationed an Ironworks employee nearby the aetheryte to collect a toll? But again, that's really stretching logic I think.