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If your "publisher" can't handle footnotes, find a formatter who can, and fer gosh sake don't allow anyone to upload your book to the KDP (or Kobo or Apple or B&N or any other online store).
While traditional publishers can employ "Real Page Numbers," I am pretty sure that self-pubbers cannot. I did read a couple of ebooks recently that had page numbers manually inserted into the text (one was a PDF review copy, the other a Guttenberg Project reprise of a public domain translation. I wouldn't advise your doing that. It didn't bother me, but I can imagine its bothering some readers.
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