I'm guessing that that Churning Mists and Dravanian Forelands have existed prior to the Dragonsong war back when Dragon-elezen relationship was peaceful? It make sense that we're charged in Chruning Mists since it's the moogles that're maintaining the area and probably need the gil to make repairs, etc.

Anyx Trine remains a mystery since it's controlled by Hraesvalgr's brood, unless dragon's secretly like trading then I don't know what's the lore reason for them to charge us gil.