I had a conversation about this very topic recently, here is the advice I got:
Headings get totally different treatment in HTML5, we have to throw away everything we knew about this from HTML4/XHTML.
In earlier versions of HTML we only had headings (h1 - h6), there are no other sectioning elements at all. That is why we had to be very careful about our usage of the h1 tag, and there was always controversy regarding it usage.
In HTML5 the sectioning is much more powerful. We have a whole bunch of new elements for sectioning and the algorithm used to generate the outline is far more complex, and flexible. In short, it no longer matters how many h1 tags we have on a page.
We must still adhere to a structured approach and be careful to generate the right outline (one that reflects the proper structure of the document), and this is what this theme does.
To conclude and clarify, in HTML5 it doesn't matter if there is multiple h1 tags on a page, what matters is how they are used in conjunction with the other sectioning elements, and that the outline produced represents the correct structure of the document.