I think it was written with the intention of having multiple routes.I didn't know there were multiple routes through "Tales of a Sea Hawk". Some minor variants, such as exactly how you get Silehard's treasure collection from the Bonaire pirates, yes (buy them, threaten the boss, or capture the ship), and a few different ways to get from Bonaire to San Juan after you're washed overboard.
It probably ended up with less than there were meant to be.
I also suspect different parts were written by different programmers.
No wonder then that it's messy...