Firstly, I salute the theme author for putting a lot of time and effort into this: clearly, this is a guy who cares about his work. It's a clean layout with well thought-out features.
However... let me be blunt: this theme should be removed from the WordPress repository. It is not a theme: it is a plugin. And this "theme" breaks every possible rule of sensible architecture imaginable. What is going on here is that the controller and model layers of the application have been forced into the view layer. This is a gross perversion of MVC with dire consequences. You can't disable portions of it like you can disable plugins, and because it weaves itself into the core application with stuff like custom post-types, it becomes nearly impossible to disable the theme to change your site's skin.
I could go on, but the point is that this theme does things that would not be allowed in any sensible software project: WordPress already plays far too loosely with architecture, but this theme is trouble, and I would strongly advise people to avoid using any theme that abuses the view layer in this way: it will eventually cause your site to collapse from the inside-out. User beware.