There is no sense in using fences only on empty desktop!
And yet that is exactly where you will find the icons that are 'fenced' by Fences.
jan_kro ... An option which alters the z-order of Fences can be a good idea and at the same time cause issues with other programs, just as others affect and are affected by z-order conflicts.
Maybe as a 'for advanced users' tweak, perhaps...