The system partition is a read only partition that gets updated only in firmware updates.
Apps can also be packaged on that partition.
Since you can't delete files from it, you cmhave the ability to disable a system application.
That deletes the updates (which are on the data partition) then disables the app.
Because I thought that was more of a "you pay us to make your app unremovable preinstalled on all of our phones"-thing rather than anything technical.
But what happens is that there isn't any way using just the device to reset it back to factory defaults, and that's a problem now. If your average joe can uninstall the play store by accident, they then can't get it reinstalled again without a PC and some technical knowhow.
By making it so you can only "disable" preinstalled apps, you limit the damage that can be done, and because of partitions you don't really harm the user at all (because that space wouldn't be reclaimed if fully deleted anyway).
It's also why most "preinstalled" apps are now just a 4kb placeholder that makes google play go and download the latest version of the app the second it's connected, so if you "disable" it you are only left with a 4kb "skeleton" of an app there.