Well placing it at the end works, but some scripts use a counter to set the range of ships/items to generate; I dunno about the ships-script itself, but itis like this: If you cut a ship out and place it somewhere else, underneath the Galleon e.g, a script with a counter grabs the next ship in the line:
Grab range from Ship 1 + random 3
that'd create a Ship from Type 1 + a random value between 1 and 3, so it could be Types 4, 3, 2, 1.
NOW: If you cut out Ship 2, Ship 3 will become 2 and so on.... If e.g the Script is set to generate SMALL SHIPS and Ship 4 is a Gunboat, you cut one Ship out and place it somewhere else, another Ship takes the place. Ship 5 would be a war galleon or something with big-ass cannons on it, it would slide down by 1 and be ship 4 / in the middle of all the small Ships you'd encounter a friggin war ship.
That's why you have to use CanEncounter or DUPLICATE a Ship and give it the ID of the BlackPearl -> Ship is (internally) still BlackPearl, but in the Game it's called and looks like a Schooner or something -> Problem solved. Then you take the Original BlackPearl make a new Ship off it, at the very Bottom of the script and tha's that.
But as I said before, I don't know if any Scripts use this way, I've seen it in the RPGutilie script, for generating a Ship for the player. Ketch + Random 3.