I think you’ve convinced me that it’s a slightly more complicated problem than I initially gave it credit for; thank you for that!
I think you could solve for the disparate community theme problem by also requiring title match for mergers. You could probably also solve for it by having a 2-way merger whitelist on links. E.g community A and B both maintain lists of “similar” communities and then if A’s list contains B and vice-versa they would merge.
Comment moderation I got nothing though. That’s a tough one.