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There is no such thing as an ibooks spec. And if there were is would be irrelevant since calibre outpus epub not ibooks.
The only spec I know of is the epub one and that most emphatically does not *require* footnotes to be in aside elements. The only thing it *recommends* -- and note that recommends does not mean requires, is marking footnotes using epub:type annotations.
Which incidentally it is trivial to do by a bit of postprocessing of the epub output calibre generates if you really want to. calibre marks footnotes and links to them with clear class names, when converting from docx. Just create a couple of saved searches in the calibre editor/Sigil to find those and add the epub:type annotations -- nad there you go. epub 3 footnotes at the click of button.
All that said, I have nothing against adding epub 3 output support to calibre, I just dont see it as worth my time. And iBooks requiring epub:type annotations to popup footnotes is not going to change my opinion on that, I'm afraid.
But as darryl said, calibre is open source, patches are welcome. I'm even willing to provide guidance on implementation if needed.
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