From the thread Blackbeard Missing from Isla de Muerta, it seems there's already one instance where, if you're playing a character that also shows up as an NPC, the game takes notice.
Less drastic results could occur if you play a character who is also an NPC in a side quest. For a bit of fun, put these where they need to be, play free-play as Claire Larrouse, then see what happens if you go to San Juan tavern...

Less drastic results could occur if you play a character who is also an NPC in a side quest. For a bit of fun, put these where they need to be, play free-play as Claire Larrouse, then see what happens if you go to San Juan tavern...
