If you have too many passengers then you won't get the options to take the captain prisoner or make him an officer, but it shouldn't prevent him from appearing.
"compile.log" says this:
Code:
CreateCharacter -> character Location fantom character <0> can invalide model(napitan) or animation(man)
LAi_CreateFantomCharacter -> CreateCharacter return false
That came from function 'CreateCharacter' and presumably means that it can't find model "napitan". That model ought to be in the Beta 4.0 Part 2 Contents archive.
@UnwantedNewborn: did you precisely follow the installation instructions from the first post of this thread?
Mod Release - Build 14 Beta 4.1 WIP [Last Update: 25 May 2018][Beta 28 May 2018]
And have you installed any other mods besides those listed in that post?