Thanks, Terisa and David. I'll try the new version of the plugin.
The extra spans are not very nice in the code, but, indeed, they provide a much better display on the Kobo. As I keep only the ODT sources and the last epub I built, this is not a real issue.
But maybe something could be done to prevent people from blindly modifying their epubs with some Calibre plugins (or sometimes Sigil). When a book has been modified by several users, it can become a terrible mess of embedded spans (plus blockquotes added with Sigil...)...
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