So, on a thread on the bug on “the website that shall not be named”, someone found some quest IDs that, through console commands, could (at least temporarily) somewhat stop the effects of the bug.
Just in case that website were to somehow go down permanently tomorrow, I’m documenting these exact console commands here for redundancy’s sake.
completequest 2c0fd9 completequest 98b4e resetquest 2c0fd9 resetquest 98b4e setstage 2c0fd9 10 setstage 98b4e 10
When used in this exact order, I and others started encountering hostile NPCs onboard boarded ships again.
Credit goes to user Otherwise_Distance92 on the aforementioned “site that shall not be named”.
Edit: had to correct the quest IDs because some “b’s” went missing while transferring text from my iOS photo library. Whoops
I’ve tried using this fix multiple times but it’s never worked for me on my current save sadly. I’ve just given up on boarding ships until NG+ hopefully.