System caches and Safari caches are different animals.
System caches include font caches, kernel extension caches, and so on. They can be flushed regularly, but usually there's no reason to. If there is a need to--for example, if you install a new kernel extension--the cache is flushed and rebuilt when the computer reboots.
If I recall correctly, rebooting with extensions off (holding down the SHIFT key during reboot) also flushes the system caches, which is part of the reason why it takes longer for the computer to finish booting.
