Make sure mFlags is synced properly in WindowConfiguration

The previous logic doesn't have the logic to distinguish "off" and
"undefined" for mFlags. This CL solves this issue by introducing
a variable dedicated to always on top. See b/110383970 for more
background.

Bug: 110383970
Test: atest WindowConfigurationTests
Test: go/wm-smoke
Change-Id: Ia4fe8f43e5f6d65d68b1257951b1770a49af35bc