all of the backups - across all users - all run at once. This can create a huge disk i/o usage because all of those backups are trying to run at the same time.
I think it would be better logic for /usr/local/cpanel/whostmgr/docroot/cgi/softaculous/do_backups.php to do one user's backup, wait for it to finish, and then move on to the next backup.