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Epubcheck, like Calibre, is a work in progress. Again like Calibre, I think it is supported by volunteers.
Just because it has limitations is no excuse to not use it. Until something better comes along, I think anyone generating Epubs should use it as the before-mentioned sanity check. And if you don't like the way it works - volunteer some of your time to make it better.
Epubs need good tools to reach their potential - and for the moment Epubcheck is the best we have.
Robert
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