I suspect you're intentionally missing the point and just want to argue (hm, that would seem obvious given your very first senctence in this discussion). Still, in the off chance that you're serious, some quick points:
Double-clicking on a file in Dolphin/Thunar/Nautilus == desktop win.
Double-clicking on some list in a custom GUI == desktop pain.
"All your other points are made moot by the export appliance feature."
I covered this in my previous message. Just imagine if you were forced to store all your OpenOffice documents (or Emacs or Vim or whatever) in a custom database, and were forced to export every time you wanted to attach one to an email or back up to a NAS. As I said, it's is a step in the right direction, but it still sucks.
"And of course an exported VM can be imported on another machine."
By "system" I meant VMWare, Xen, Virt-Manager, etc. Can any other virtualization system import a VirtualBox appliance?
"Using the same file for different things is just a bad idea."
Sometimes true, often false. Imagine if you had to store each layer in a separate Gimp file. Or had to keep mp3 data in one file and its ID3 tags in another. It would be horrible. Maybe read again the upsides and downsides I mentioned in the previous message?