Are you able to start flatpak octave from the command line with
flatpak run org.octave.Octave
app/libexec/octave/6.2.0/exec/x86_64-pc-linux-gnu/octave-gui is the address of the executable within the flatpak sandbox. The second address is the address starting from the root directory. They are the same file. Running
from the command line will not start flatpak octave.