I think the gil thing is a gameplay concession. I don't mind at all. While Kugane and Radz would definitely have exchanges and accept it, the "commemorative" one gil coins from a long time ago are stated to be minted in the Eorzean city states. They also bear images of Nymeia as well as the leaders of the three city states. While Endwalker Garlemald is in no condition to refuse foreign currency (unless you're a fan of telophoroi bank tellers,) it would seem a bit odd to me that earlier they would accept and deal with such diverse coins bearing the images of enemy generals.

Hingashi definitely still uses koban, and you can find "dated Radz-at-Han coins" in the hinterlands for some reason... Those may or may not have been replaced by gil. And of course, there are the plethora of Bozjan coins and various alliance raid coins. What in the world did they need coins for in Aglaia?

As for Allagan nodes in places like Azys Lla... I'll just headcanon that they take all your coins and press them back out as those little flattened pennies you get from museums.