Ideally, I would like to be able to display the emulated Game Boy Advance on one display, and the GameCube on another in full screen, and use a different shader for each. An example would be running the dolphin core on one display with crt-royale, and running the vba-m core on another with agb001-gba-color-motionblur. Using Dolphin, and VBA-M, two displays in full screen can be achieved by using extended display on Windows 10, moving a each window into a different display and utilizing the Alt+Enter key combination. I would imagine that being able to do this in RetroArch would require two separate instances open at the same time, that could run full screen on each display, and could connect to each other by toggling an option of some sort.
Below is a link to a post explaining how to set up the Game Boy Advance and GameCube link using the emulators that the cores are based on.