A short update:
Here's a reply I got from their Customer Service:
"Feedbooks doesn't just distribute ebooks: our technology also generates on the fly any book in any format (EPUB, Mobipocket, PDF). This enables users to personnalise their PDFs for example (text size, choice of fonts, etc.) and also allows us to constantly improve the quality of the books we generate (formats like EPUB are still new and evolving quickly).
For this reason, we need to have as our source not only the text but also its structure (parts, chapters, sections), instead of an end format. To distribute your books on Feedbooks, you must therefore create the appropriate structure in our online editor, then paste the text from Word or any text file to provide us with the necessary information. You only need to do this once; after you've created your book via our interface, you can generate any format you like, and obtain a valid, good-looking ebook which can be read on any reading system.
As for the footnote function, once you're in the editing tab, click on the yellow square to add a footnote after the word you've chosen. A window will pop up, in which you can enter the text of the footnote. Then click on Insert."
Their answer skips over the fact that I already have a valid EPUB with a valid structure (chapters and subchapters via /h1 /h2 and so on), not just a slab of text.
It seems ridiculous that one has to format the text all over again using clunky web based tools, but that's how it is.
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