Hi,
generally you can use another linux distro, but there are caveats linked to the heads firmware:
(1) To implement the authenticated boot, the heads firmware verifies whether an ISO is on its whitelist, similar to an activated secureboot. So, it won’t just boot any ISO. This is the problem you encountered.
(2) The firmware expects a /boot partition with a grub folder. It extracts the linux kernel to boot from the grub configuration to create its own boot entry. So, whatever you install must present it that (all regular distros should offer such configuration).
My suggestion is that you just install the Ubuntu that Nitrokey offers as installation alternative to Qubes. Just follow the documentation for it, but perhaps just let is use half your disc (e.g. you could install PopOS from Ubuntu later and use it alongside Ubuntu, or delete Ubuntu after PopOS boots).
I had a similar problem to you, when I installed Arch on a nitropad. My install notes are geared for Arch users, but you may get an idea how to approach what you want.
The range of distros supported by heads directly does get larger, but your experience shows PopOS is not recognised in the firmware yet.