If your original download from Amazon was azw3, you could use the KindleUnpack plugin to get the ePub rather than using a calibre conversion. I purchased this book from Kobo and it renders without noticeable issues on my Kobos.
You might also want to try kepubify to convert external to calibre and then sending that kepub.epub file to your Kobo. The KTE extended driver has had some issues reported.
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