It's impossible for an X app to draw on top of the Unity shell because
the Unity shell is part of Compiz and designed to always draw after app
windows (hence appears on top).

If you want the appearance of Unity not being on top then you need to
modify the Unity code so that it doesn't draw itself on top, or not draw
itself at all under certain conditions.

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https://bugs.launchpad.net/bugs/734908

Title:
  Unity is visible on top of fullscreen apps

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