By default, software has a sandboxed location that is exposed to the host in `~/.var/app/[APP]`.

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.