The yacht is definitely the VIS file. I've noticed it before. Wouldn't surprise me if that was the case with the Refugee Quad as well.
Having a look at the level and the VIS, it seems like it should be working properly. Both of the access corridors, 302NARaf and 302NARap, are listed as visible from 302NARr, which is the Serroco side shown in your pics. So it seems like that shouldb't be the problem.
Looks to me like the problem is the corridors aren't visible from each other. I don't see 302narp visible from 302naraf or 302naraf visible from 302narp in the file.
Yeah, that was it. I'll add 302 to my fixes, but I've attached it for immediate use if you want. You'll have to rename it to .vis since Deadly Stream doesn't allow attachments of weird KOTOR file formats.
I still haven't looked at the yacht for the same reason I didn't look at it before - the ship has lots of rooms and it's annoying. But I'll get to it, possibly.
I remember years ago running through either the first or second one in the beta release. I actually liked your original design because there was no proper hangar - the ship was just there on the street and anybody could see it as they walked by. It was like the planet is so polluted and overdeveloped they don't really have the space for that or even care to anymore. Like Nar Shaddaa. Some of that wonkiness might've been due to your skill level at the time, but I actually liked that. I really like the new one too, though. It's by far the most polished and looks exactly how you'd expect one of the game's hangars to look.
Like VP said, the more tools the better. We just got KOTORMax, MDLEdit, and an MDLOps, and now this year there's a whole line of new tools in the works for other areas that were in need of updates. It's nice that the community is still so active even after 15 years.
And a Linux version would be most welcome. I run Mint on my laptop, and seriously the only reason I ever boot into Windows is if I need to run KOTOR Tool. Either that or I overcome my laziness and go to my desktop. So with a KOTOR Tool replacement, even just being able to look at the files would further enable my laziness.