The point is about a marked-up document's concept of 'itself as a document', and how this rarely matches to an HTML document, which is a container for the document as well as a bunch of not-document things (navigation header) and para-document things (section sidebar, preview embeds and popups).
I think all of the color stuff is meant to illustrate (or should I say, ink) the bad design revealed by this disparity. I didn't actually get it, but I've always been a <b>bold</b> sort of person, <strong>strong</strong> just seems like another way to say the same thing, which caught on as a fad.
But HTML having markup for documents inside of documents? Strikes me as a good idea. What I don't know is if that's blue or chartreuse.