Wordproccessing. Export and reformat according to the page size you want, or buy everyone ereaders (or at least phones / tablets with the Pocketbook app).
Actual ebooks don't really have footnotes or endnotes the way paper, PDFs, DTP or word processing has. A consequence of being paginated html were the "page" size is unknown at design time or to the distribution. Real ebooks don't even work quite the same as HTML on a web site either.
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