Interesting, not being a Kobo owner had never heard of a kepub. Thanks for the information.
However I still fail to see where any of this has any real relevance to this plugin.

The behaviour described of different page numbering on the Kobo between an epub resulting from a calibre conversion vs a Kobo store sourced "kepub" has been well explained, they are different formats that the Kobo has a differing feature sets available for. But as this plugin from a device perspective only has relevance to Kindle owners with mobi format books it is completely unrelated.
So the only association of any kind I can think of related to this whole Kobo discussion is a user wanting to see a page count in their calibre library that is similar to what they will see on their Kobo. But as has just been explained, a Kobo user already gets differing page counts depending on whether it is an epub or a kepub. And no-one seems to have an idea how exactly either is computed

. If you want a page count based on 1000 characters (ADE style), you already have the ability to choose that in the algorithms for ePub.
So I don't see anywhere to go with this as a possible enhancement, sorry!