You do want LibreOffice, Gimp, VLC, and your webbrowser to be able to save and open their respective media files in your home folder, right? And you want might want them to be able to actually work together, right? Such as opening a file you downloaded in the browser. Whether the file chooser is inside your application or outside your application doesn't make it any safer, it's the fact that the application has the ability to open and read/write the files.
What you seem disturbed by is that one application can access configuration and state data belonging to another application. Because they are just files, belonging to the same user. Well, I suppose if such a policy made you feel better, you could always change the AppArmor profiles to only allow an application to modify its own dotfiles, dotdirectory, e.g., fooapp can't touch ~/.* except ~/.fooapp. That's not a terrible idea, although if you are so distrustful of it to begin with and still want to run it you should probably sandbox it in its own filesystem altogether. And this will break some interoperability.