Just to let you know though that its really rare that flatpak is used for cli's. I think I mentioned it in my comment too or if not, my apologies but flatpak is used mostly in gui's.

I doubt its efficacy here, they might be more useful if you provide a whole jupyter / browser gui though but a lot o f us run it just in cli so I doubt flatpak.

I didn't mean to say that flatpak was the right tool for this job, I seriously don't know too much to comment and so I'd prefer if you could ask someone definitely experienced regarding it.

My reasoning for flatpak was chunking support (that I think is rare in appimage) and easier gpu integration (I think) compared to docker, though my reasoning might be flawed since flatpak isn't mostly used with cli.

Oh no worries on flatpak - I always like investigating things I'm not familar with :)