When he tapped on a link to a footnote reference, it displayed the footnote text in what looked like a pop-up window
...
I gotta say, the pop-up display was very cool. Looking at the raw code of the epub, I can see where the links to the footnote references are coded as:
From the forums:
<a epub:type="noteref" href="#citationxx">link text</a>
<aside epub:type="footnote"><div epub:type="footnote" id="citationxx"><p>reference text blah blah blah</p></div></aside>
http://www.idpf.org/accessibility/guidelines/content/xhtml/notes.php