I think what you are seeing might be because the ePub reader uses GPOS kerning, but the KePub reader uses old-style 'kern' tables for kerning.
Most fonts seem to come only with GPOS kerning tables. If you want the kerning to work with the KePub reader then you need to add old-style 'kern' tables to the font. You can use fontforge to add the missing tables. (i.e. so the font will have both GPOS and 'kern' tables, and it will then work with both ePub and KePub readers.)
Edit: Actually, on looking closer, the letters seem to be kerned okay in the KePub version, so I guess the 'kern' tables must be present. I have EB Garamond on my Glo (in ttf format with 'kern' tables added) and it doesn't have this problem though.
Edit2: I think if the font is embedded in the book then you won't be able to select a sideloaded font with the same name. Do you have a link to the actual version of the font you have embedded? It looks a little different to the EB Garamond I have. (EBGaramond-0.016.zip from
https://bitbucket.org/georgd/eb-garamond/downloads.)