As a user, I'd like to give Krita/Libreoffice permissions for ~/Documents and Tor Browser permissions for ~/Downloads. I don't know yet of a user-friendly method to achieve that.
[1] https://docs.flatpak.org/en/latest/sandbox-permissions.html#...
The filesystem permissions are a bit more fine-grained than "all of home or nothing". Your two examples are already possible to achieve by granting filesystem access to xdg-documents or xdg-downloads.
Signal let's you save attachments anywhere on disk, but only if you manually navigate to ~/Downloads, does it actually save (in a way visible and accessible outside of the app). You just gotta know.
I forgot what exactly the problem was with Vscode(/ium), but it also has a catch like that. You just gotta know.
Flatpak turns out to be the best compromise between distribution and cross distro compatibility, but there's still some low hanging fruit that could be improved.
