Having fences roll up behind opened apps is a major bummer for me.
Fences is a desktop icon management tool. By definition it works with the desktop icons at desktop level where they exist.
Microsoft determined the order at which focus of "what becomes on top" is arranged.
What you need to ask yourself is..."does any program on the planet allow the change of level of a desktop icon to be shown above any open window?"
The answer will be "no." The Microsoft Windows desktop 'Z-Order' cannot be readily messed with simply because Normal Expected Functioning [system management of input] will be lost and confusion will reign.
Windowblinds was one of the first to push the boundaries...with the option to lock a window on top of others, with or without focus [a handy tool], and Fences 'peak' enabling the seeing of the icons under a window is also a 'messing with the Z-order', however the shifting of click-through focus really should not be what it's about.
Docking programs are available for a windows-level display of launch icons as they are entirely different to something operating at the Desktop Icons level. 