cause user caches arent just used by the browsers, user caches are mostly used by the system, browser caches are used by browsers(BTW, cleaning out user caches also makes it so that when you start typing in a browser and it usually starts trying to fill in the url for you, if you clean user caches, it wont do it, itll be like reinstalling the os and having an unused browser.), and some unimportant(which are usually important in one way or another) are kept in user caches, very few setttings, also some directory access and such, so its like breaking in your computer again, kinda.
dont delete the systems hidden .ds store files, or core.xxx files, dont delete links between documents and their applications, most of its common sense.
system cache deals more with the ui, like locations of icons and buttons in apps and in the finder, also stuff like locations of icons in toolbar, sidebar, dock. deleting system caches may result in an empty dock, messed up looking finder or apps, menu bar items missing, system preference panes missing or in the wrong place, stuff like that.