I am not 100% sure, but I remember the Black Pearl being called a black frigate in a dialogue during the quest where you first learn about her.
Maybe this is where this comes from?
Gordon Carpenter, the man who meets you in Falaise de Fleur port and takes you to the tavern, refers to the
Black Pearl as "black frigate" once during his dialog. Otherwise he calls it "a boat with black sails" or just "ship". Henry Peat, who sits in a house in Falaise de Fleur and tells you the first part of the story, merely calls it "pirate ship" or just "ship". Owey McDorey, who gives you the chest, and the cursed pirates who take it from you, don't mention the
Black Pearl at all. By comparison, the
Mefisto is referred to as "frigate" or "black frigate" by various people, so if any ship was previously going to be identified as "Black Frigate", that's the more likely candidate. As I said, in the 17th century, "frigate" could mean all sorts of warship, so the fact that some dialog calls the
Black Pearl (or
Mefisto) a "black frigate" is not much evidence that either ship should formally have been identified as "Black Frigate".
Fun fact, if you look through the vanilla game files you can find a ship called "Fearless", a naval coloured Black Pearl stock but without a poop deck. Never appeared in the game (most likely for the original script before Disney).
"Fearless" was not a variant of "Black Pearl". It exists in the modded game with different textures as "RN_Warship", "PO_Warship" and "SP_Warship", and in fact "PO_Warship" even uses texture file "Fearless.tga.tx", though the texture has been changed. It's simple to copy the stock "Fearless.tga.tx" into the modded game, and so here's how the ship looks:
For comparison, here's the stock "Black Pearl", present in the modded game as "Lineship1":
"Fearless" has a more pronounced poop deck than "Black Pearl", and a flat, vertical stern. It lacks the jib sails and has only one square sail on the mizzen mast.
I was under the impression that the concept of a cursed ship being the final boss, or even being in the game at all, was a last-minute addition from when Disney converted Sea Dogs II into a POTC tie-in.
That is my impression as well. The whole chapter about the cursed coins appears to have been tacked on as an afterthought - the quest code is in "both_reaction.c" whereas the rest of the storyline quest code is in "quests_reaction.c", and the questbook entry for the coins is almost at the end of the questbook file "quests_text.txt". (Only the tutorial questbook entries are after the cursed coin section, and the tutorial quest code is also in "both_reaction.c", so the tutorial at the start of the game might also be a late addition.)
I wonder if "Fearless" was originally intended to be Silehard's flagship? Perhaps it was replaced by the big 100 gun ship to give him something more different from the
Black Pearl, or perhaps it was replaced because "Fearless" is a fairly poor quality model even by stock game standards, but it was never completely removed.