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span id="kobo.1.1" and so on is added by the plugin. This is the main point that makes an epub to an kepub. Those elements are used as reference points for highlights, annotations, etc.
The interesting point is how the "special class for chapter title paragraphs" is declared in the css. There seems to be something that the epub rendering engine honors and the kepub rendering engine does not. Maybe you can change this in the calibre settings in a way both engines can deal with.
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