Interesting. Given the examples I posted above, did you try wrapping the footnotes themselves in a section tag immediately after the hr?
See:
Code:
Footnotes Section
-------------------------
<section role="doc-footnotes" epub:type="footnotes">
\1
</section>
This was taken from one of the aria to epub type guides as a good example of how to do it.
Using a section tag will allow it to be included in an auto generated chapter outline by the accessibility reader allowing users to quickly find that section, or more likely skip over its contents (if they chose to already follow the footnote links themselves).