A while since I did this, but in my /etc/skel, I only have the Maildir directory. I assume that postfix ot dovercot created the new, cur and tmp directories on first access. No permission problems there. My Maildirs are owned bt the relevant user with permissons 700.
You may need to edit dovecot.conf, but looking at mine, it doesn't look like it probably needs changing, so I think you may be correct in saying thta main.cf is where the action is.