As far as security goes, couldn't this be solved by a separate tool, in the good ol' Unix style?
And it would be up to downstream to handle AppImage files with it for sandboxing, or not.
And it would be up to downstream to handle AppImage files with it for sandboxing, or not.
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
As in yes, i see nothing that prevents you from applying existing sandboxing techniques around Appimage distributed software.