It does technically the same, except by default names the .pvm "copy of <original name>.pvm", and by default tries to save it to the same folder, you can change all this in the Save As panel, but it's an added step, also, it registers the VM (if I'm not mistaken) in the VM machine list.
As I don't want neither of that, and just want to keep a copy on a different drive which I can simply drop in and replace, I rather copy the .pvm.