The Zen book says to use the override system anywhere I see "Classic" and "Template_Default".
The book actually says you can determine where to put your overrides folders & files anywhere you see either a classic or template_default sub-folder. There's
only one template_default folder, and it's in includes/templates.

The tutorials you're reading are assuming you are creating your own template and gives a starting point by suggesting you use the stylesheet from either the includes/templates/classic or includes/templates/template_default, and the template_info.php file associated with whichever you chose. By installing the barebones template, this step has been done for you.

The chart shows that you have 10 places where you can put your barebones (your custom template) in includes/templates, includes/languages, and includes/modules. When you create those folders in languages and modules,
they should be named exactly as your barebones folder in includes/templates.

Hope this helps! I know I struggled with learning this.