The third solution wouldn't cause extra communication. If you're subbed to a community that follows other communities, you receive all the posts once. That's the same as if you followed all of those communities yourself.

If your server hosts communities that follow others, that would still be the same as having users on your server follow those servers. It's the same amount of communication.

I'm assuming you were talking about this comment. That doesn't explain why merging communities is bad, only why you may not want to do it. Which would always be an option. Having the option to merge duplicate communities doesn't mean you can't maintain similar communities without merging them.