I can think of a work-around but it is clumsy as all get-out.
You could convert the incoming document to PDF, annotate, and send that PDF file back to the author with your notes. Another variation, something can probably be done, is if you can keep original paginated page numbers displayed in the converted PDF (or any other converted format for the e-reader). Then you could note the original page # in your notes, allowing you to send the notes back with the original document.
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