Most things already work. You know, desktops need to start with that, they need to implement popups for these permissions. And I guess apps also dont ask for permissions yet (like they do with Pipewire access), they just take it or fail.

So its again a problem of adapted apps.

Storage is all stored in ~/.var/app/ and could be duplicated etc if you really want to. That would require some hacking, but you could have multiple profiles for apps. Tbh this is not hard to do at all, just rename the app folder to "appname-profile" and rename the active folder back to the apps name.

A GUI for that would be interesting.

Browsers are a big example of good native packaging, as they get most attention. But for example on Debian, or Ubuntu, or many other platforms, I would prefer to use Flatpak Firefox (if firefox didnt have their deb repo now).

Chromium is hacky as Flatpak as the Sandbox is imcompatible and needed to be replaced.

For firefox there is no statement about this, hopefully soon. I use native browsers for the same reason as you.