Replace, not patch
Cleanup will not rewrite a few lines of load.php. If you apply a clean, core is swapped from an official tree whose hashes match the local database. wp-config.php is never replaced. See how the engine treats the site as data.
Official maps
WordPress core integrity check
When local checksums for your WordPress version are present, Cleanr Engine compares core PHP to official MD5 maps. Modified files and unexpected PHP under wp-admin / wp-includes become findings. Missing checksums do not abort the scan.