Is Karlach related to plot?
If not, i would really like to know when she boarded the ship.
That does feel more like game plot than background lore to me, and so of course could change utterly between EA and the full release.
My own theory on the Karlach stuff is that she boarded the nautiloid while it was in the hells in the prologue, and was possibly part of Zhalk’s boarding party (I’m assuming she needed support from other Hellish denizens to get onto the ship given her lack of wings, though there may be ways she could manage without it, and so wasn’t part of the boarding party at all but was just nearby). Either way it is weird she got tadpoled so quickly. Perhaps she was captured and quickly implanted because the mindflayers saw her potential to help fight Zariel’s minions, or perhaps her tadpole’s original host was killed in the fight with the devils or githyanki and desperate for a new body somehow crawled into her before she realised what was going on.
Whatever, it seems she intentionally hid on the ship rather than accidentally being brought along when it jumped back to the material plane and Zariel knew somehow that she’d deserted. Perhaps Zariel contacted her - or tried to - after the nautiloid left. And on finding Karlach unwilling to return, Zariel cast about for other options and fortuitously found a group of travellers and a paladin of Tyr at a nearby toll house under attack by gnolls and on the verge of defeat. She offered them a bargain to save their lives on condition that they kill Karlach, sealed with their souls, and the rest is history. Possibly Karlach herself was even holed up at the toll house with the others after escaping the crash and Zariel wanted them to turn on her. I can’t recall exactly what was said about Karlach and the gnolls in the game.
I admit I have my problems with this story, as well as the Karlach quest itself, but I’m guessing that this was an area that wasn’t really worked on for EA and, assuming Karlach is indeed a companion, will get tweaked, fleshed out and tightened up for full release so I’m not worrying about it overmuch.