The question is what happens when the phone has actual hardware buttons and you port the OS to it which has virtual buttons in it...that gets weird I think...
Are you seriously considering the fact that virtual buttons will be always present regardless of the presence of hardware buttons ?
The way he showed the virtual buttons last night made them seem highly customizable by each app for different purposes. So once app creators start making these custom virtual buttons for their apps, they will not have multiple versions of their app for phones with and without hardware buttons...
its not really a big deal. I have no doubts you'll be able to hide them on phones that have hardware buttons.