No, it's atomic. It's just not important if separate databases are not atomic to each other when you recover from backups, you will still have data loss and an inconsistent state. I.e. things that should be in the database missing, and that shouldn't be overwriting missing IDs, etc. Backups cannot be strongly consistent, so you have to take the exact same approaches to deal with this whether you store everything in a single database or in two separate ones.