Think it wise (ie, gonna have to), piddle with settings, cron, etc. to get auto the way you want it running when it runs. The default settings for automated backups, the first time you run them should be 'ignored', but found that not to be always true. Example: course hidden or hasn't been changed in X days/months, etc. may or may not be included in the first run of auto.
Also, best to tinker with settings, set the timing to close to present, then run the cli script for autobackups. After it completes, see what's missing from the designated directory and compare with courses in the Moodle (hidden or un-changed).
One way to clean that up, is clean up the Moodle. Remove any already archived courses (hidden), etc.. During a semester, I'd almost call that mission difficult. :|
As far as eradicating from the 'course backup area', that could involve tweaking DB as well - use caution cause it's intertwined with the new file system.
I understand the goal ... smaller site backups, etc.., but if this 'other area' is a symlink in file system repo OR just a directory outside of anything Moodle, then when moving/restoring one might have to re-construct some pieces. Not hard to do ... just gotta remember add that to the list of things to do (before/after) moving a site.
'spirit of sharing'
Ken