Are regions and features automatically created when creating a sub subtheme? I want to inherit everything from a main theme except the layout.
When I create the .info file and specify which regions and features I want are these generated automatically by drupal or do I have to specify each one in a separate .tpl file like the diagram below?
Yes, you will enherit everything unless you modify the page.tpl.php file located in /sites/all/themes/yourtheme/template folder.

The page.tpl.php file contains all block regions. Thus, you should modify this file if you want to add, remove, or move regions. 

If you want to resize or theme a region, it's all css. As you will see in page.tpl.php, the regions will have a div class or id.