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In the end, after a few days of experiments, this was my final solution:
- reverting to a normal EPUB;
- eliminating all epub:type attributes;
- placing all the notes at the end of a document in a section by themselves;
- preceding every note by their number, like in a normal essay;
- placing a link to the specific note on every <sup> number;
- placing a backlink to the <sup> number on every note number (basically the two <sup> numbers link themselves to each other).
Concerning the small caps, I simulated them by writing all that I needed in caps and reducing the size of the letters after the first one to small. Frankly it looks much better than whatever the kobo was producing with the correct CSS.
The funny thing is that both the kindle app and the actual kindle ereader still understand, somehow, that those are notes, so if the user clicks on the note number they open as popups, and this doesn't happen with the backlinks. The kobo, on the contrary, doesn't open any of these links as popups, but it's fine, everything's still perfectly comprehensible, and frankly it even looks better.
It's a small step (backwards) for the EPUB standard, but it's a giant leap for my document.
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