I think it's ok, as long as federation still works and migration is sorted out. The problem with centralisation is the control that can give. If there's a mechanism to move a community or user to a new instance without too much disruption, then the users maintain control and have recourse if the operators do something unpopular.
Mastodon has a pretty good system that automatically moves people's follows to your new account if you move. We need something like that for Lemmy.