Following may (not) be a bug - uncertain if function behaviour is intended.
Automated course backup function duplicates course backups, does not remove old course versions when saveto destination is not the course default dir and does not skip hidden courses.
1. login as admin
2. go to Home > Settings block > Course > Backups > Automated backup setup or http://yourmoodle.com/admin/settings.php?section=automated
3. use follow settings
Execute at: 00
Automated backup storage: Specified directory for automated backups
Save to: path something like /home/directoryoutsidewebroot
4. save changes
5. wait period for automated course backups to run, then go to saveto directory specified above; note multiple versions of each course backup.