Seems one way to solve the "always on top" is to give the ability to hide all open windows - similar to Win-D. Win-D works fine UNTIL you open another window. Then it loses all the open windows that it closed.
As it is now. Win-D puts all windows onto the task bar. Hit Win-D again and they all pop back up where they were. GREAT.
NOW, lets use that with Fences. Win-D hides all the windows, go to a fence and it expands, select what you want to open. So far, so good!!!
ok, now I want that window I JUST OPENED to be on top of all the previously closed window. I hit Win-D again to restore all the windows and, WHAT???, NOTHING pops back up. When I opened that selection from Fences Windows "forgot" about all the other windows that had previously been open.
If something similar could be written into Fences such that a key sequence would run a Stardock command to hide all the windows then hit that same sequence again to restore them, with the added bonus of anything activated in a Fence would remain on the TOP of the restored windows would be very much worthwhile. It may be a little bit more to do than if the Fence would stay on top, but, I wouldn't have to manually move all my windows out of the way!!!