Flatpak is not an OS. Weird question.
Both variants are very similar. The Guix tool comes with a "guix system" command, which lets you build Guix System containers, container images, system images, qemu VM images, qemu VM scripts, etc. The only command that won't work on a "foreign" distro is "guix system reconfigure" --- but that's only a "guix system init /" away ;)