This doesn’t check all files in /, because certain directories change frequently, like /home and /var. Instead it defaults to checking /bin, /boot (which should be empty since PureBoot systems require a separate /boot partition, but it’s here just in case), /lib /sbin, and /usr.
But you can edit the list of directories it scans to add or remove what it checks. For instance if you want to set this up to run at each boot, but don’t like how long it takes, you could remove /usr entirely (or replace it with /usr/bin, /usr/lib and /usr/sbin). That would of course reduce protection from tampering but it would also dramatically increase scanning time.