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This is a wild guess (David or Peter might know better), but the formats use two different rendering engines and I'd guess Kobo mainly takes what they're given when it comes to the RMSDK which is used for ePub's and only really digs into it if there's a bug of some sort. I'd assume they spend most of their development time working on the Access renderer instead where they can have more control of things in general. I personally prefer kePub and since using Calibre to send my ePub's to the device is set up to convert things on the fly leaving the original ePub in my library unchanged I don't even notice that I have to convert things.
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