Debian (to a huge degree) and Ubuntu (to a somewhat lesser degree) prioritize stability over newness, so it makes sense that they are usually years behind. And PTB can be had from NeuroDebian reasonably fresh. But also, I only test with Octave versions bundled with a recommended Ubuntu release, so with flatpak et al. you are on your own there as well. And PTB won’t use Octave/Matlab features that aren’t supported in the oldest Octave version we officially support, e.g., atm. what’s in Ubuntu 20.04 / Octave 5.2.
Your --filesystem=host will probably be made a tad useless because some directories are black-listed, as the footnotes and links describe, e.g., /lib, /lib32, /lib64, /bin, /sbin, /usr, /boot, /root, /tmp, /etc, /app, /run, /proc, /sys, /dev, /var
Without etc, sys, dev some low-level stuff, or special device access (USB, HID, serial ports etc., low-level access to AMD/NVidia gpu’s), realtime optimizations, PTB would be quite hamstrung already. Also no access to many libraries it needs, unless they’d be included in the octave flatpak.
And there’s probably more switches required, like --devices=all and various other permissions to make it work. Don’t know if snaps would work better, but the goal of all these app distribution systems is not only ease of distribution/updates outside the regular distribution package management, but also rather strict security sandboxing / isolation, as such 3rd party stores are considered way less trustworthy than what comes from the distributions own package repositories.
I saw your post on octave-users discourse though, forgot most of it already. Good if Opticka would be able to run on Octave. But yeah, flatpak would probably barely work even if you manage to disable almost all sandboxing.