I guess not, some skills are bound to be unlocked after completing a certain amount of main story. Never tried otherwise though, i kept both run in parellel...region wise, but i believe i completed enough side missions on each session to unlock every skill if that was the case but some skills still remained locked.
The same pirate mark i got once in my radar but when i reached that place driving, i found none! except two local ladies sitting on their knees on sand facing each other..heads down...and between them a tombstone was there!!! I believed those two killed that poor b****d meantine and buried him fresh!
, i felt that it was cold blooded murder, two ladies looked one wife and daughter...so it was conspiracy...
it also seemed they were fake mourning, so i planted a C4 right between them...and blew them sky high to pieces. that poor pirate is now RIP