I've had some issues with getting DeoVR (both steam and oculus versions) to work well in alpha channel with Virtual Desktop. When running it through virtual desktop the "background" becomes black. If you then enable passthrough in VD you need to set the color to black. However this isn't very good as shadows become all weird.
A quick solution to this would be the ability to change the applied background color to something like green, instead of black.
Of course, running DeoVR locally on the Quest3 will work better, but with huge VR video libraries with 20+GB videos this isn't really possible due to Quest3 internal storage limitations.