In my current random map game, I wiped out the Yithril except for its sovereign, Warlord Verga. He is sitting on a transport ship one square away from the beach. I can't touch him since I don't have a transport ship.
Later on, I discovered the Resoln sovereign sitting in a transport ship but on the beach. At least I was able to attack him. I moved on and attacked the closest Resoln city; at first, the (sunk) transport ship showed up as defending the city. I canceled and clicked on a different part of the city and was able to have a normal combat (no sign of the ghost ship).
I have a saved game that shows Verga on his boat where he has remained since I discovered him just south of one of his former cities. Unfortunately, I did not get a saved game that showed the phantom boat defender.
I hope my future random map games don't include transport ships; this is the only time I've seen them on a random map.
https://www.dropbox.com/s/efgr5z4hniufkot/Verga%20retired%20living%20on%20boat.EleSav