So far I've tried to disable grass and enabling antialiasing transparency on nvidia control panel. I'm not even sure if those settings would change anything, but I gave it a shot and it didn't work.
I'm downloading an update for my GTX 980ti right now, and I'm running GOG's version on Windows 10. I'll let you guys know once I'm done with the driver update
Edit: Updating the driver didn't help. Just would like emphasize that, as mentioned in the mod thread, I added the TXI file posted by DarthParametric here, and changed the blending mode from punchthrough to additive, and that made transparency kick in. That doesn't really fix the issue because it will show transparent buildings
Edit 2: Here's my swkotor.ini if it's of any help:
Edit 3: I've enabled cheats and went to check at least one location of each "world". All skyboxes are fine. I only have issues with the buildings in the Upper City of Taris