ISO 14389-1 (PDF/UA-1) defines accessible PDF.
As PDF/UA-1 stands on the foundation of ISO 32000-1 it too is a requisite reference for anyone having an interest or need to deploy accessible PDF.
Additional reference information is available at AIIM.
Two documents are currently available.
The third (PDF/UA-1 Technical Implementation Guide: Understanding ISO 32000-1 (pdf 1.7)) is still under development.
"Achieving WCAG 2.0 with PDF/UA"
"PDF/UA Technical Implementation Guide"
As to footnote (or endnote) these must role map to the PDF element "Note".
For "Note" ISO 332000-1 informs us that:
Note is a standard inline level structure element.
The associated description -
(Note) An item of explanatory text, such as a footnote or an endnote, that is referred to from within the body of the document.
It may have a label (structure type Lbl; see “List Elements” in 18.104.22.168, “Block-Level Structure Elements”) as a child.
The note may be included as a child of the structure element in the body text that refers to it, or it may be included elsewhere (such as in an endnotes section) and accessed by means of a reference (structure type Reference).
Tagged PDF does not prescribe the placement of footnotes in the page content order.
They may be either inline or at the end of the page, at the discretion of the conforming writer.
If the conforming writer takes the approach of placing the "Note" element's content at the end of the page then the "Link" element with the requisite children "Link - OBJR" and content (optionally placed under an inline grouping element such as "Span").
For cross-reference PDF provides the standard inline level structure element "Reference".
As to any AT application establishing "standards" for any technology/file format accessibility that is rather like putting the cart in front of the horse eh?
Fortunately one AT application is proactively coding for compliance with the ISO Standard for accessible PDF (ISO 14289). This happens to be NVDA.
David, Thank you, that enough reading for a few days...
As CtDave points out, ISO 14389-1 (PDF/UA-1) is the definitive reference. But for some of us it is too technical for practical day-to-day application. I am looking forward to the publication of something like "PDF/UA for Dummies" but that might be awhile. I tag the footnote as "Note", and place it as close as practical in the document structure to the associated reference without disrupting the reading flow - usually this is immediately following the paragraph containing the reference. "Note" is an inline element so it has to be inside another tag like a paragraph. As best I can tell this meets WCAG 2.0.