What does the Kindle have to do with the Kobo or ADE?
That thread on FBReader for the Kindle has nothing at all to do with the problem of embedded fonts in an ePub not working on the Kobo.
The problem as I see it is that the menu's font selection is overriding the ePub's embedded fonts. An option in the font selection that says ePub default would do the trick by just turning off CSS override for the fonts.
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