Flatpak applications under Linux get their little sandboxes under ~/.var/app/$application-id where they can create whatever they want and the user can remove it from there when needed. Except for that, any other path that the app can access is decleared in the permissions; or the user is very well aware, because he picked the file via filechooser (portal).

Soma macOS applications can use similar scheme, under ~/Library/Containers/$application-id, but for the user more difficult to know which one is supposed to and which isn't.