How do you guys get software that is not in your distribution’s repositories?
Nothing in theory makes that an issue of flatpaks and snap, just that both rely on different means to interact with the host system that have been woefully slow to implement. If enough protocols are developed a flatpak or snap should be as capable as a native app with the safety benefits for free.
If you look through the desktop portals GitHub, it seems to be a mess of bikeshedding, mostly on the part of a small number of people on the flatpak side. Canonical seem to have been working around this in snaps by writing their own interfaces as stopgaps until the desktop portals catch up, probably because they got such pushback when the similar frustration on the display server side resulted in them releasing mir with its own protocol until the Wayland folks could get their act together.