That won’t work. Flatpak is for GUI applications.
You could also use e.g. a Github Action / Gitlab Runner.
@aaronrolls I made a short tutorial for how to install a Debian 11 VM with ARM arch on an x64 system: More Librem 5 apps! – A tutorial to compile Flutter apps for Librem 5 on x64 machine Just a few commands to get the system working. Just head to the Debian section and ignore everything else.