Only idea I had in mind would be to have the post go to a "home" community and all other communities pull the comments from that one and submit their own comments to that one. If the "home" community has rules that the others roughly follow that might help filter the extreme ends out so you don't just get constant de-federation.

Content allowed on instances:

Instance 1: Content A, B
Instance 2: Content B only
Instance 3: Content B, C

By making instance 2 the home for the post, which by it's own rules only allows content that both instance 1 and 3 allow themselves, you filter out the content which 1 and 3 would hate. Of course, this puts the moderation burden on instance 2. You could still allow instances 1 and 3 to have their own comments which instance 2 doesn't allow, but only they will see those comments.

IDK, I feel I'm starting to see why Lemmy works the way it does. I'll post in !lemmy_support@lemmy.ml if I get a better idea. :)