I started the game way back with the Joker Mod, but I wanted to try yours as well. I downloaded the Mod yesterday (9/22) and installed it with a freshly unpacked version of the game, downloaded 9/19, so everything should be latest and greatest.
Three observations:
1) Looks like the Brooke replay assumes Dark - I don't remember the forcefulness from my earlier plays - I thought the force her versus let her go at her own pace was a choice. But, hey, it's been probably two years since I played that scene originally, so may be mistaken.
2) It would be helpful if the Taboo toggle turned green when on, red when off (or something like that) since I couldn't find a visual indicator that it was on or off in the stats/cheats pages. Yes, it became obvious when I went back an started the dialogue (thought it was on, but wasn't), but if that's an "easy" thing, it might be nice. If it's a pain in the ass and not worth it thing, so be it.
3) Autosaves are not autosaving with your Mod. I looked over the features commentary, looked for toggles, but couldn't find anything that indicated whether this was a conscious decision on your part, or some kind of glitch. I've never seen them turned off in other games I've played with your mods, so I'm wondering if your own autosave feature at the end of the chapter is interacting oddly with the built in autosave. Autosaves are a feature I like since I can just go there to look at the alternate choices and decide if I want to go that route or not; without it, I guess I'd have to use a bunch of other save slots or quicksaves that might override other quicksaves I wanted to keep. Autosave was working fine with the Joker Mod, and, yes, I'm absolutely certain there is no cross contamination.
My $0.02. Keep up the good work.