We as pirates collect skulls to hand to the order of souls.
In my idea.. The Skeletons have been doing some collecting of their own!
Those sunken shipwrecks you see are from attacks from skeleton Galleons. Poor souls who lost their lives to the undead.
These lost souls were meant to go to the ferry of the damned but the Skeletons have stolen their souls and kept them stowed away on their ship where they meddle in the otherworldly and unnatural.
My idea brings this to life.
Inside the prison cells of roaming skeleton Galleons is a container holding the soul of an Npc.
Jump aboard the ship and break the lock by slashing or shooting it. Grab the container and hand it over to the mysterious stranger in the tavern, who in turn brings it to the pirate lord who assists them to finding their way to the ferry of the damned.
It's an exclusive activity for pirates who put themselves at risk diving into an enemy vessel.
The reason the soul containers never float to the surface in a sunken Galleon is because its locked away on the ship.
Now we have a reason to hop aboard!