This might be a delayed response, but would it not be possible to act as a process that injects what it wants to display directly into the graphics card, similar to the tool com.dec05eba.gpu_screen_recorder
and should it detect that discord is in focus on the same display as it shows up on normally, then it stops displaying anything
Otherwise display on screen in selected location as configured
Also the flatpak fails to remember config options like "Only show users who are speaking" and "Enable join/leave notifications"