It works by actually deleting the data from the system partition, that's not a big deal. But what happens is that there isn't any way using just the device to

It works by actually deleting the data from the system partition, that's not a big deal. 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.