Time Machine backups of Checkout Stores are NOT 100% reliable and should not be the exclusive backup mechanism.
When Checkout is running, Time Machine may fail to copy parts of the database that are currently in use. As a result, the Time Machine backup of the database may be corrupt. The only reliable method to backup a Checkout store is to use the backup process in Store Administration.
Backup files created from the Store Administration backup process can be reliably backed up using Time Machine.