How are you setting the window to "Always on top"? Can you provide specific repro steps?
I haven't used unity much but for most WM if you right click on their button in the task bar you get an option to keep it above all other windows. An example is xfce which allows this.
The window manager hint for this is _NET_WM_STATE is _NET_WM_STATE_ABOVE as can be seen here http://standards.freedesktop.org/wm-spec/wm-spec-latest.html.
Other methods to trigger the window menu: alt+space, alt+right click
Forcing a window to always be on top will definitely confuse the client as it has its own internal Z order stack. Definitely a bug, but not something we're going to fix in the short term.
Nothing extracted yet.
When one window is set to "Always on top" (ex: friends list) and another window is under it but focused (ex: main window) clicks on the always on top window will be "handled" by the focused window. For example, if I put my friends list on top of the "Play" button in my library my click will go "through" the friends list and launch the game. For other windows (ex: firefox) the click is handled by the friends list as expected.