Moving to and fro between Snap and flatpack(Gnome follows this) will change the development philosophy.
Flatpak was laid by Leonard Potterhead, who broke too many POSIX decorums because he believed in fast Linux development process.
Following is sum up for the question, but the question is very broad, so trying to pick up few points.
- Snap is has single corporate backup Canonical while Flatpak has many.
- Snap is strictly following the POSIX philosophy.
- Flatpak is no server process while snappy has [in most of cases].
- Flatpak has library dependencies from Freedesktop,KDE,GNOME while
snap has Base distro snap.
- Flatpak cannot run without sandboxing, while snap is optional.
- Flatpak is optimized for air-gapped (offline) machines (the kind Ed
Snowden uses) but snap is not.
- Flatpak is fully decentral without the central gatekeepers while in
case of snap, it is no.(a single app store)
- Flatpak allows application authors to self-host application with no
functionality loss while in snap it does not.
Still researching on this question, fewer answers