On opensuse tumbleweed that is linux based I was able to perform firmware upgrades in the terminal, but not using the flatpak.
For performing firmware upgrades using opensuse linux the following instructions should be added to Installing nitropy With pipx - Nitrokey Documentation
To install nitropy run the following command and say yes to installing all of the dependencies:
sudo zypper install python3-pynitrokey python311-importlib-metadata
After nitropy was installed using the above command to update the firmware on the nitrokey 3A run the following command:
sudo nitropy nk3 update