We take logical backups, not physical, and mysqldump is the best option for that. Having logical backups means we can do logical diffs as well (see https://youtu.be/Fe2oLZ4CWD4?t=951), and we've added table checksum support to mysqldump in our branch of MySQL (https://github.com/facebook/mysql-5.6/commit/54acbbf915935a0...)