any setting described in config-dist.php is configurable in your config.php; plus, any Moodle setting can be forced via config.php locking it from further modifications e.g. via UI.
Automated backup folder is configured via backup_auto_destination in Site administration > Courses > Backups > Automated backup setup i.e. $CFG->backup_auto_destination = 'D:/sagecache/backup';.
Up to you to force it or just edit that setting via WebUI (/admin/settings.php?section=automated).