Since the original post, I've tried using two different solutions for forcing windows to stay on top and neither works with the ModernMix windows. I've tried both "Window On Top" and also the "Always On Top" script using AutoHotKey. I imagine that at their heart both of these programs work the same way as I expect pretty much every other program that does this must. I surmise that if I were continue to try other programs I'd always get the same results where they wouldn't be compatible.
If this is not a feature that ModernMix will add out-right then could the compatibility issue be fixed that prevents the third party applications from making the window stay on top?
Otherwise, has anyone else tried to accomplish this and had any better luck than I have? Maybe there is some way to get this to work without Stardock engineering a fix for it?