Well after some testing and looking thought the forums i understood how it work.The free passage deal work fine, until you go any sector of Port Ceto.If you seen in any, the deal is broken ,and all Pirates a red now.Well didnt you think that a deal with a Pirate would be fair dont you?Unluckly the original Underrail, factions quests system is different in DLC.You just cant work on 2 or more faction in DLC,and wont gain acces to the Pirate shops and quests working with Aegis corp.And the decision moment is Proffesor kidnapping quest.This is last point to decide which faction you with(not sure about could you work with native).So i advise you just kill them all.Yes i know with every named character death your soul will scream in horror, you will loose a part a story,and maybe some (NO NO no0oooo0) unique items and feats.But you can handle it.
PS Ferryman always mooving from location to another location in black sea,so you need just wait and seek him other place.
PSS sorry for my bad english.