I just figured out a way to distinguish between notes added by CC to original documents and those that appear as part of the original document.

Notes that are part of the original document may be written like this:

hi rend="vertical-align: superscript; font-size: 80%;"

The number of the footnote would go inside that <hi rend> tag. Then, at the bottom of the document, the note, encoded like this:

p rend="font-size: 80%;

... and the note would go inside that <p> tag. For notes added in by CC, we can just use the generic <note> tag.