Since Goverlay released a flatpak few days ago I've meaning to use it.
Got it working for steam through flatseal but it doesn't work for heroic no matter what I do, I tried both flatseal and in-app settings but nothing works.
This what I used for flatpak steam:
Filesystem: xdg-config/MangoHud:ro
Variable: MANGOHUD=1
but doesn't work on flatpak heroic