Oh thank you sheson the lord and saviour!!
I'm guessing simply deactivating Open Cities Skyrim.esp with a mod manager isn't enough on ver 3.0
I was going insane trying to figure out what the problem was, went through the entire 112 pages of this thread and 2 hours of fruitless Googling to find anything related to this.
Deleting the esp solves the issue, did the first pass, restored it and did a second pass. Time to test this out in-game, wish me luck