Both checksum verification and WordPress reinstallation are done without loading WordPress itself for security reasons. Reinstallation should not affect any site data, but users will be prompted to create a backup before proceeding if they want (just in case).
Important note: this feature cannot check index.php, wp-config.php, or other similar files that contain installation-specific data and don’t have a reference checksum. Checking these files will require a different feature, and that’s a tale for another time.