At one level, I absolutely HATE the duplication that splits comments.
At another level, I recognize that splitting comments is most of the point of community. Making all people comment on all posts essentially breaks the entire concept of developing a community-specific culture of rules and norms.
In theory you could have each community "adopt" posts, creating community-owned discussions against universal posts. That would be OK. Then instead of cross-post duplication you could look at a single post and see all of the communities that have adopted discussion on it.
Maybe that's the solution.