My understanding is that "system app" just means it's baked into the ROM. So it's not actually possible to uninstall it without flashing. Disabling removes it from all the application lists except the one in settings where you can re-enable it. [0] My guess is that the rooted uninstall is removing it from all system lists. But the binary is still there in your ROM, unless you've flashed a new ROM that removes it.

[0] This is also why the disable button dialog discusses uninstalling the updates to an application. Because updates are obviously not written into the ROM; they're in normal application storage.