Okay I finally got around to doing this. I removed Alternate Start completely and Scrap Everything. I did the full intro legit, did the first set of stuff with Codsworth. I got to the workbench and scrapped enough to build the city desk. I
still don't have any theme tags when I try to set up themes sadly.
I guess my next thing is to try to disable everything but SS2? I'm not sure city themes are worth it, but I also don't know what else is borked up in SS2 or other stuff. Everything seems to be working though recruitment is kind of slower than I remember from SS1. Been able to plow through the SS2 quests with one hiccup (had to restart when I built plots ahead of the quest and it screwed up everything...)