Well IMO, they really improved on the system/theme part of Drupal with D7 by making it more modular and separating the document template (html.tpl) from the content template (page.tpl). Prior to D7 you used to have page.tpl.php that did everything. Now that they have a clear separation, it's very simple to change from a xhtml doc and do an html5 doc or better yet some mobile device friendly doc.
As far as content within the html.tpl file, it doesn't seem to be content html that is included, just reference to variable blocks and a "skip to main content link". I've never used the skip link so I'm not sure why it's there but perhaps because us developers might take it out if we had the chance
I haven't looked or tried to access page variables from within the html template but it could be that the variables you want to access from within html.tpl.php are only available from within page.tpl.php.
Also, don't worry about being dense when it comes to figuring this stuff out. If you keep at it, it will start to make sense. Also since D7 has changed the game so much over D6, the documentation is still being worked on. There is a "Drupal way" of doing things and it takes a while to get the philosophy of how things are done. I would start with a simple vanilla Drupal 7 site and maybe just look at the default Bartik theme and look at the template.php file. Within that file you'll see bunch of preprocessor functions that run when a page is generated. Some of them add classes to navigational links or change the way the breadcrumbs work or add classes to the body tag. Reviewing that will give you an idea of how things are done. It might seem daunting at first but also know that when you create a custom theme you can have as many or as few of these functions as you need. I'm in the midst of developing a site right now for a graphic design and it doesn't even have a template.php file.... I don't need one.
- If you need to do some server side processing to create a variable that you'll want to grab on the page, template.php is a good place to do it within the THEME-NAME_preprocess_html() function or the THEME-NAME_preprocess_page() function. This is an old post but it describes the idea behind it: http://drupal.org/node/11811
Keep plugging away and it will be rewarding. Drupal is like a box of lego bricks. You can make it do anything but you have to do the engineering and put the pieces together to do so.