This inclines me towards AppImage, as the whole point is to have the easiest experience for the user.
https://www.reddit.com/r/linux/comments/4l20yt/ive_been_play...
And it would be up to downstream to handle AppImage files with it for sandboxing, or not.
As in yes, i see nothing that prevents you from applying existing sandboxing techniques around Appimage distributed software.
If Flatpak's main selling point is security, then it would be better served as as a sandboxing tool for AppImage rather than falling for NIH syndroming as is unfortunately too common in Red Hat's world.
Observe flatpak becoming part of Fedora shortly, and then Poettering style "nudging" implemented to get Debian and the rest to adopt it.
[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=813308