That makes sense if the application is the only program that needs to interact with the data. For example: If you have a drawing or photo editing program. You might have downloaded an image from the internet or from your camera. Then you make some edits. Afterwards you want to send the image to someone else via e-mail, which is another program.

If neither compatibility nor resources are of concern then integrating true Mandatory Access Control into both the UX and the entire tech stack would be the best way forward.

This isn't always easy and a lot of software on flathub is old-ish, so people tend to open up permissions since it's difficult to implement all these features properly. In my experience people will rarely stand in your way if you try to improve a package.

Nothing should change, all installations and addons go to the ~/.var directory. When you launch the application, yes it can start reading and writing to arbitrary places on disk, which is why I make it a habit of first launching Flatseal to modify permissions and know exactly what it can and can't do and reach.

I actually vastly prefer this methodology with what we have right now, but if it or something else adopted an application/directory methodology as you described I'd be elated.

Most software needs access to user files. Since most applications aren't written with Flatpak in mind, they will attempt to load files using their own file browser, meaning that for the application to function at all it needs to have access to swaths of extra data. You can see what data the application can access either via FlatSeal or in whatever "app store" you're using. Often it'll be your entire home directory.

The software that is designed with Flatpak in mind will use XDG Desktop Portals, where the host displays a file browser and then hooks it up to the sandboxed app so it has access only to that file or directory.

Note that you can't magic your way out of this. You can't eg. wait for the program to request access to a file before displaying a "Program wants access to this file. Allow/Deny" because the program doesn't know if this file exists, and the user wouldn't be able to navigate to it via the program's bespoke file browser since it doesn't have access to directories or their contents.

More and more I have found myself simply using podman and dockerfiles finding that building nix systems simply gets error prone and annoying and all the containerization systems leave a lot to be desired. Though I have some custom scripts for utilizing btrfs snapshots to create different nix store snap shots for containers or vms running with nix stores with virtiofs. This works quite well but not ready to be released and fiddly when things break and requires BTRFS.

I do agree flatpak and friends are not great though.

It's also not doing runtime sandboxing at all. Isolated builds protect you from supply chain attacks but not malware or vulns in the actual code, and they don't do anything for closed source apps.

Flatpak runs everything in a container with access limited to what is declared in the manifest and you can restrict it even more with Flatseal. It's not as secure as a Firecracker VM but it works way better than any other package system on Linux when it comes to security and distro independence.