For what its worth (and I'm no designer): I really like the mobile version of your design. The text is easy readable, the sections clear and there is no annoying clutter.
He definitely means once all the weird column/row effects and text are gone. The site becomes simply, with your header, your content wrapper, and the content. It's a lot nicer at that point.
The longer I look at the desktop version, the more I like it, but my first reaction was not good. It's too much. (I'm a hacker, not a designer, btw)