Hmm, I don't disagree with the fragmentation but that's the nature of any new social platform. It's also been proven out that eventually one or two communities for a topic will become the dominant one with the others falling into disuse.
Attempting to merge communities early or artificially will cause moderator strife as minor disagreements balloon. Especially in a multireddit community where no one mod(team) has absolute control.
I don't have a reason from a technical point of view, but from a social one. Forcing communities and instances together early will only cause strife. After a few years where two communities have a track record and proven 'behavior' would the multireddit not cause issue.