Update system application overlay api

Convert the SYSTEM_FLAG into a PRIVATE_FLAG and expose a method for
setting it.

This API is easier to use since it makes it possible to setup the
LayoutParams before having access to the Window.

Bug: 171177581
Test: atest CtsWindowManagerDeviceTestCases:HideOverlayWindowsTest
Change-Id: I0bf3857e3dbf67f8833b3b3847b2253d31b9d4a5