When I get books with goofy font sizes like that, I load up calibre and connect the device, select the book, and use the KoboUtilities plugin to "set reader font for selected books".
For some reason, the default font size for epubs is drastically different than kepubs, and this is the only way I've found to make one size align with the other without editing the books or changing font size on the device every time I switch between them.
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