1. I'd have to double check that specific case, but when I was getting started, I saw that most quests similar to that (zombie farm, bjornin's half-ogres, reevor's rats) all had new creature files specifically for that since they had unique scripting, so the randomizer doesn't consider them valid things to randomize. When it's installed, it reads the area files for the relevant sections, so it'd pick up any creatures added or changed before installing the randomizer (as long as they were the normal CREs and not newly created creatures).
2. I'm not familiar with BuTcHeRy, and I didn't do a lot of testing with other mods installed, but I'm not sure if it would matter in the case of SCS. This doesn't make any changes to CRE files, just area files, so if SCS is making changes to the AI in the CRE files there'd be no conflict. So if BuTcHeRy sets the spawns after SCS, I guess after SCS would be fine for this too?
3. I didn't do a full run of the trilogy doing every quest, but I did a decent amount of playtesting and I didn't run into any broken quests, but if one gets reported that would be my top priority to fix.
4. That makes sense. The components are actually filtered by the found game type so an EET install wouldn't be able to choose the BG1/2 components, but I can definitely clarify that in the readme.