Well, that was surprisingly easy a solution. Should have figured that out myself.
Either way, I'm done now, has been fun playing with the mod and the game did indeed feel more complete.
However, while they're probably already reported, I still feel the need to point out a few of the noteworthy bugs I encountered while playing.
1. Somewhere after/on Telos (but only after I got my stuff back from the TSF) I lost all the items from my inventory (or rather, I noticed that only then, dunno when exactly it happened) with the exception of the items my party members had currently equipped, as well as credits, chemicals, parts for crafting. It was not exactly game-breaking since I managed to get a somewhat decent basic equipment back with the help of the console, merchants and some crafting, but it was nonetheless highly demotivating and annoying. Actually, I remember having tried this mod once before already with a different character, but that time, I noticed that it happened already when on the Ebon Hawk right after destroying Peragus. That totally killed my motivation to play on.
2. I was attacked by the Red Eclipse thrice. The first time was alright and played out okay. The second and third attack happened somewhere when I was near the Swoop Racing place. It all happened again with cutscene and all, though no questlog entry. The guys near the ship who talk to you and then attack spawned again (twice, obviously), but nobody else did, including the people within the ship. So I could do nothing and had to use the Warp cheat to return to the "regular" Hawk Interior whenever I wanted to enter it from Nar Shadda.
3. After I got all the required HK-50-Kills and that scene played where HK-47 tortured the captured unit and learned where the factory was, after a few seconds, the screen faded to black and nothing happened, no matter how long I waited. I could fix it by saving the game and loading that save.
4. Only a minor thing, but since I am someone who likes an orderly questlog, it still annoyed me a bit. The Lost in the Shadows quest was never noted as finished. For the record, I persuaded Kaevee to the dark side, then went to explore the Enclave Ruins, found the mercenary corpses, went to find Vrook, but left him with the mercenaries and then joined Azkul and attacked Khoonda.