1. I really like the boxes, for one, because they are visually striking and make it easier to distinguish different sections of the navigation from each other. I also like the color scheme.
2. OK, as for resizing the browser: yes, very very very bad. It’s bad because it gives you a little scare, like your computer is about to crash or it’s been infected with adware. People will close the window and hit the back button and never return. Of course your site doesn’t actually make the browser crash or install spyware, but it will give people that feeling of concern that will make them just prefer to visit one of the other 6 billion web pages out there. Also I don’t appreciate it that when I leave your site I still don’t have my browser’s scroll bar–have you thought of that? Maybe maybe you can self-justify taking away the user’s scrollbar when they’re on your site (maybe). But how can you say it’s ok to take away apart of their browser when they’re not on your site?
3. The scroll bar in the middle: that’s a frame. I know it’s not the old-fashioned html frame, but it’s functionally the exact same thing. Frames have gone out of style for many reasons, all having to do with the fact that they make the site less usable. Just read Jakob Nielsen’s writings on the subject. Yes, the current default browser setup of scrollbar on the right side of the page in the web browser is vastly preferable to users as demonstrated in numerous usability studies (again, Google Jakob Nielsen and frames). Also, the frame prevents you from making the most out of your screen real estate by forcing the little bottom navbar into view when you would rather use that screen space for reading content. In short, it’s an imposition on visitors, even if it was intended as precisely the opposite.