Pretty sure he meant "rooted" in the sense of "inserted exploits into the codebase". In some sense that's much worse that mere root access to the host. Such a database could, for example, phone home with all updates to tables named "passwords", etc...

And even in the more banal sense you interpreted, sure: you might not run mysql.com-sourced daemons as root. But you almost certainly run the mysql command line utility as root from time to time.