Perhaps you could contact Kobo's developers and ask them why they made the decisions they did?
As for rendering as badly as before? I tried a sample of 7 people with an epub and kepub (kepub synced from Kobo, epub downloaded from Kobo and sideloaded). The only person who read part of the ebook and noticed any differences between the two versions was myself. The rest either didn't notice or were not bothered by any differences between the two books.
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