Is it performing operating system package updates (with yum or what-have-you)?
Or is it just updating Plesk itself?
As a bonus question, if it isn't performing operating system package updates, then how does one do that with a Plesk server?
In a lot of cases, specifically on Ubuntu or Debian servers, the Plesk Updater does the task of running apt-get upgrade. Since the Plesk repositories are in /etc/apt/sources, the Updater runs apt-get upgrade to get the latest Plesk files and in the case of my Ubuntu server, do other system package updates IF those are a dependency to the plesk packages being updated.
If you don't want to rely on Plesk Updater for operation system-level security and software updates, then for Ubuntu/Debian based servers, you can use apt-get or for Red Hat servers, use yum.