You’re running the server from the Steam deck?

Because even without Flatpak, there’s plenty of other packages for different distros that are easy or easier than flatpak. You don’t have to go all the way to docker.

It’s probably best to do it eventually but it doesn’t have to be today.

The jellyfin docker is really easy to set up. And then you get the benefit of complete portability.

If you really want it as a flatpak you could attempt to build your own with up to date versions. However that would likely take longer than using an official package.