My oh my this mod has progressed. I'm glad it didn't stall, thanks again Produno.
It was strange to not see anyone already state this but when you travel to a sea city using the ship wright dialogue the party is unable to leave the city, as soon as it tries to it immediately enters the city again.
Example 1: I traveled to volantis, was unable to simply pass through volantis on foot, had to go around the other side otherwise I just kept entering the city again.
Example 2: Completely stuck in Bravoos because there is no land to maneuver away from. As soon as I try to leave the city I am automatically teleprompter back into the city.
My guess is that since I still don't technically own the ships that brought me there I am not able to use them even for the short distance between Bravoos and it's port.
If you go on the water at any point without a ship then it will put you back on land or back to the nearest party. That is by design. Otherwise you wouldn't need to buy or use ships.