As with the majority of writers, I prepare my manuscript in MS Word, using both Mac and Windows versions. My current book requires a great deal of research, thus many hundreds of footnotes. We've chosen to record the notes as footnotes to keep them with the relevant text while writing, but will convert to endnotes when the manuscript is complete. Like most, I'm anxiously awaiting native support for foot/endnotes in AfPub, but have found what looks to be a nice workaround in NoteStripper by editorium.com.
NoteStripper is a Word macro that allows me to strip the notes (footnotes and/or endnotes) and place them at the end of the Word document. The main text retains the (unlinked) superscripts that relate to the numbered notes. I can then have two documents: one with the main text and the superscripted references to the endnotes; the other the list of numbered notes. Both documents retain their original formatting, and can be placed in AfPub separately (unlinked).
I did a search in this forum for NoteStripper and for emporium.com, but found only one reference to the latter, seemingly not related to the footnotes issue. Hopefully, this adds a bit of value to the discussion. If not, then just "Hi! I'm Len. Happy to make my first post!"