It is worrisome that the device reboots. It sounds like installation is interrupted and something triggers reboot. But great that you managed to make it work.

Now, we do have setuid application installed - flatpak-bwrap . It doesn't have to be setuid while you install apps. So, if someone who can trigger reboots by installation or removal could strip setuid from /usr/libexec/flatpak-bwrap and try again, that would be helpful. If you get reboots even then, its bug of the OS (or RAM pressure). Just don't forget to make setuid again, otherwise flatpak will not work.