The --rsync option of app-portage/mirrorselect should support repos.conf, both as file and as directory. It should check if an entry "gentoo" exists in repos.conf and, if it exists, modify its sync-uri and if it does not exist, create the entry (or file, if repos.conf is a directory) with updated sync-uri.
*** This bug has been marked as a duplicate of bug 600572 ***