When automated backups are executed a message is sent to the admin. This message generates a log in the lgacy log store after the changes made in MDL-40913 with a course id of SITEID. Since this is a write action , it marks the course as modified and the automated backup never skips it, irrespective of the skip settings for backup.

The problem here is, in legacy logs we used to use SITEID as courseid for system level actions which is wrong.
The best solution here would be to modify the $sender in backup messages to use no_reply_user, instead of admin.