System security applies to the environment in which MySQL is installed—the hardware, network topology, and operating system. For example, if your MySQL database is installed on a machine where dozens of people have root access, they can bypass your excellent database security through direct manipulation of the MySQL database and executable files.
A user in the system security context differs from a user in the MySQL database security context. Specifically, a user in a system security context is any individual with access to operating system processes—via either direct access or across the network.