I would like to do this too, but how much clean-up will there be? I guess that depends, eh?
E.g. the websites for my add-on domains are currently in a dir I created: "~/other_sites". I guess if nothing else, I'll be moving the files for the new primary domain to "/public_html", and moving the current files there to "/other_sites/[old_primary]"? Andddd, god knows what else I'll need to fix after that. Hm, wonder if this is worth the trouble.