The empty template isn't generating anything more than the required components that specify it as a Windows store app. It's not a template anymore without those components. Furthermore, Visual Studio generates even more code after compilation to do things like bind XAML with its codebehind.
A lot of the code is making calls to WinRT libraries, e.g to render a window and register tile updates. You could in theory come up with all that code for yourself, but it probably wouldn't look much different to what's already generated for you as you have to make calls to WinRT in a certain pattern (or else your app is terminated), and you would probably end up just looking at the templates anyway in the end. There's really no point.
I'd suggest you just look at the empty template and trace through stuff if you really want to learn.