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I have checked the working of the kepub file, and I really can't see a lot of difference. Beside the encryption which must be different and a couple of addition to the toc.ncx file, I really don't see any substantial changes.
There is a css and js (Javascript) folder with files for android (I guess from their name). There must be some small changes to the html file, but the files being encrypted I can't compare them. Why not release your kepub format specs and we could create our own files? I could add converter into my app. Not the best solution, but it might make some impatient people less "annoying".
From what I can hear, I guess that kobo created their own engine to go around Adobe restrictions. Maybe that is why some function like dictionary and highlighting don't work with normal epub files, because they are not processed by the same engine. They just didn't implemented it yet.
I can understand why adding functionally to an other vendor software might be a problem, things like font and etc. may be a problem, but for things like dictionary, which are not directly related I can't see why (not that I care).
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