Fences is a coralling system for Icons which are part of the Desktop and by Microsoft's design are intended to stay at that level [Z-Order].
Windows are designed/intended to be above the desktop and/or above each other as when focus is changed [again Z-order].
Fences is not designed [nor can it be] to alter the layering of Microsoft's GUI. Other Launchers are designed for that, and in Stardock's case specifically ObjectDock which can and does pop-over both the Desktop AND open Windows.
It is safe to say that Fences will never have an option to alter the z-order of the Microsoft GUI [though as soon as you say that anything can happen].
Confidence. N. That feeling you have immediately before you fully understand the situation...
PS....would I like it as an option? Yes...
[copy/pasted from https://forums.wincustomize.com/477761/page/1/#3694171 ]