Thought about ...
"We have a lot of courses in the system because our data retention policy requires us to keep two years worth of courses in the production system"
Suggest that's a choice to keep on production server. Don't think even GDPR dictates such courses need to be on XYZ server. College on West Coast USA, for example, has a new Moodle every year ... what ever is latest/greatest ... and that's the active/currently used Moodle. Something like mdl2020.tld. Last years moodle is therefore retained automagically and only admins/teachers can access - it's an archive. Maybe students too but in a kiosk kinda mode - can see but can't interact with old courses, etc. Think they keep 5 such servers ... so a 2018, 2017, and a 2016 are also online.
You could do something similar ... all courses not currently active could be xferred to a 'mdlarchive.tld' box thus reducing autobackup processing. The mdlarchive.tld box wouldn't need daily autobackup ... maybe just one run to have a course backup. That server set to 'nochange' and 'nomail' just in case.
'spirit of sharing', Ken