You don't explicitly state it, but I assume you are starting with a CBR or CBZ. If that is wrong, maybe the other comments will be.
My first question on this is always: Why are you converting? The Kobo ereaders handle both CBR and CBZ without any conversion. And you can zoom the images when reading.
Your last post tells me that KCC generates the file as ".kepub.epub" and expects you to send that to the device. When you add that to calibre, it is added as an epub. And any later processing is done as an epub. Sending that to the Kobo device will mean the device sees an epub. You need the double extension for it to be seen as a kepub. You could use the KoboTouchExtended driver to send it, and that will do the extension fixing.
I'm surprised that the formatting was different when the comic was sent as an epub instead of kepub. I can't think of what could be in the books code that would do this. It's been a whiles since I tried, but I have put a kepub in the device as an epub with no errors in formatting. Maybe it is something in the way the images are done.
When I tried KCC after the Kobo support was added, I couldn't convince myself it was better than the calibre conversion. Or just using CBR/CBZ. There is no way to turn the image resizing off, so that meant I had to generate a version for each Kobo device I have. And there is no way to generate a generic epub. And as kepubs support zooming, using the original images should work.
I should add that I don't read comics. I have done some playing with them on the Kobo devices in response to questions like yours and some bug reports. So, I might have missed something important for someone who does read a lot of comics.
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