by Séverin Terrier.
Hi Stefan,
Sorry i don't provide a direct solution for you.
But perhaps you can vote/comment for MDL-52050, that could finally help for your need.
You can also create a little bash script, calling in a loop (with all needed course IDs) the /admin/cli/backup.php script. But it will use your current settings for backups (so you need to modify them before and after).
Séverin