This marketing page suggests it is now possible to create these properly in Indesign: http://www.adobe.com/accessibility/products/indesign/faq.html
But there doesn't seem to be any reference to it anywhere else.
I'm trying to create an accessible PDF of a book, with the plan being to do this with all books from now onwards. I have followed all the guidelines in the document produced for Indesign CS5.5 (it doesn't seem to have been updated?): http://wwwimages.adobe.com/www.adobe.com/content/dam/Adobe/en/products/indesign/pdfs/indes ign-cs55-accessibility-whitepa…
In the exported PDF, one of the obvious problems is that footnotes are tagged as 'Note' but positioned at the bottom of the page, i.e. screen readers will get to the bottom of the page and then read the footnotes, then move onto the next page (rather than associate the footnote with the text it relates to). Acrobat Pro rightly flags the Logical Reading Order as 'Needs manual check'.
Some books have 1000s of footnotes, and manually correcting Indesign's erroneous placement of the footnotes is so time-consuming as to make it unworkable.
So, what is the solution?
InDesign CC 2014.2 (10.2.0.69 x64 build)
Arcobat Pro 11.0.10
Windows 8.1