flatpak-builder build-dir --user --ccache --force-clean --install io.github.betaflight.BetaflightConfigurator.json
Then you can run it via the command line:
flatpak run io.github.betaflight.BetaflightConfigurator
or just search for the installed app on your system
Make sure you followed the additional setup specified in https://betaflight.com/docs/development/USB-Flashing