Bear in mind the Scions and WoL were also trying to go to Othard and work mostly in secret. It wouldn't have done to get found out by some Garlean spy discovering a number of people matching names and descriptions of the Warrior of Light and the Scions clambered aboard a chartered boat that travels regularly along known shipping lanes. That would be a quick ticket to getting surrounded by the whole Garlean Navy.
Imagine the message that would send... "We took out your trump card AND your attempt to go behind our back to liberate Doma, Eorzea. Now what will you do?" Taking a smuggler's ship along less traveled routes (hence running into trouble in the Sirensong Sea) was the much safer option given they wanted to hide their involvement in the Doman Liberation Front until they were ready for a head on attack.
Imagine the message that would send... "We took out your trump card AND your attempt to go behind our back to liberate Doma, Eorzea. Now what will you do?" Taking a smuggler's ship along less traveled routes (hence running into trouble in the Sirensong Sea) was the much safer option given they wanted to hide their involvement in the Doman Liberation Front until they were ready for a head on attack.
