As of right now, loot can be removed in battle; whatever doesn't take damage gets transferred to the attacking faction. I am considering changing that, though, since it's more fun when the points stay on the map.
I'll think about the ship-to-map move (something like "Embark/Disembark"?), but since you always rule the clearing with the ship, I don't think there would be a problem. They'd still be stopped by the Corvid's Snare, but it's nice to let other factions have their fun ;-)
The balance is certainly the biggest issue going forward. I've avoided the board wipe in my multi handed play testing, but I can see how it might happen. Not sure how "thematic" this is, but the Pirates actually want to Parlay (to generate loot) more than they want to destroy everyone else. Might need to reduce the number of warriors or tweak some mechanics, but hoping that the faction gives players a new way to approach the game.
Thanks for taking a look; I really appreciate having another set of eyes taking a look at everything!