What if the story splits in the beginning of stormblood allowing you to go to ala mihgo or kugane first and then reconverge later... it could explain why it seems like we start in kugane.... everyone looks at the map and sees ala mihgo right there and kugane all the way on the far side of map forgetting if you were to go to kugane it's faster to sail west from horizon... which is why the Domans keep popping up at the docks there...