After you have installed KiCAD from Flatpak using
flatpak install --from https://flathub.org/repo/appstream/org.kicad.KiCad.flatpakref
you can run it using
flatpak run org.kicad.KiCad
You can append any arguments to KiCAD, for example open a project file directly from the command line:
flatpak run org.kicad.KiCad MyProject.pro