If ARQ is turned Off and the Backup Files buttons for: Root Files, wp-admin Files and wp-includes files are not clicked again before turning ARQ back on then any WP Core files that have been changed/modified will be autorestored and/or quarantined when AutoRestore is turned back on. Most likely someone will NOT be manually changing WordPress Core files. A more likely scenario is someone will be manually modifying wp-content files (theme files) and would ONLY click the wp-content Backup Files button to backup wp-content files only. ARQ is intentionally compartmentalized by having 4 separate Backup Files buttons for this exact reason/purpose.
We will look at and test this idea and see if it can be used/applied without negative impact to website performance and that it cannot be easily beaten and that it is not redundant to what AutoRestore already does in a much more sophisticated/advanced way.