This has to be one of the worst UIs for a slide deck. "Why aren't these questions being answered?" ... "Oh, the slide advance UI changes. Too inconspicuous."
Not only that but it also makes it much easier get an overview about what things are discussed in the presentation.
I didn't bother to figure out the multi-dimensional navigation of these slides. Paraphrasing Tufte, Richard Feynman managed to write about much of physics without resorting to more than two levels of headings. I'm similarly unconvinced that multi-dimensional, nested documents are really that helpful here.
If your slide deck needs a secondary nav, it probably shouldn't be a slide deck.
-> No confusion, great overview, direct jumps with hyperlinks, easy to realize with pure HTML.