Thanks a lot! I finally figured out how to get it to work, it is only missing a --dlsym:
First to let flatpak mangohud read the config:
flatpak override --user --filesystem=xdg-config/MangoHud:ro
Then i launch VintageStory with this:
flatpak run --command="bash" at.vintagestory.VintageStory /usr/lib/extensions/vulkan/MangoHud/bin/mangohud --dlsym /app/bin/vintagestory