I finally figured out what was causing my UI to bug out so hard and make the game unplayable.
I had the game folder in my old hard drive, where I keep almost all my downloaded games. After moving the Nude Byte folder to basically anywhere on my main SSD (I tried the downloads folder and documents folder) it worked just fine and didn't make me replay the tutorial, either.
I couldn't begin to understand how it works but that's what fixed the issue I was having. Glad I can finally play an updated version of the game. I haven't played since 2.5 or something.