The whole point of flatpak is to standardize better security cross-platforms. Allowing "some other tool" to do that for you, just means most apps and most users will not take advantage of that security.
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