No, it still doesn't make any sense. On the one hand, you argue that a desktop user doesn't want to manipulate the configuration file with xmlstarlet. On the other hand, you want to use command-line completion and scp in order to mess around with your VMs. Then you complain that "there's no single thing to execute or double-click", but there is. Launch the Virtualbox GUI and you get a list of your VMs. Double click on the one you want to launch and you're done. It doesn't get easier than that. And given that Virtualbox handles all those files automatically and transparently, how would they ever get lost or out of sync? You're just making up problems that don't exist. All your other points are made moot by the "export appliance" feature, you can easily checksum, download or backup those. And of course an exported VM can be imported on another machine, that's the point.
Using the same file for different things is just a bad idea, since it just makes the file format more complex without a real benefit. Keeping different things separate is the POINT of a file system, and it would be stupid not to use it. And a hard disk image and a configuration file _are_ very different things.