MangoHud can be configured just like the instructions mentioned by the project with a few changes:
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You can either create a configuration file in:
~/.var/app/com.valvesoftware.Steam/config/MangoHud/MangoHud.conf
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Or you can give the flatpak access to filesystem on the host:
flatpak override --user --filesystem=xdg-config/MangoHud:ro com.valvesoftware.Steam
if you prefer to keep the config file there.