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I suspect what's happening here is a matter of the book cover versus the metadata cover. In calibre's file system, alongside the book you'll see "cover.jpg". This is what gets added to the book file unless you specify different options in conversion. If you unpack the KePub and inspect the converted book cover and cover.jpg, I bet they're different.
Beyond here I'm a little more fuzzy on details. As I understand it, metadata sent over to Kobo by calibre-web, as a consequence of how Kobo syncs, is the metadata shown in the UI, not what's in the book itself. The cover is included in "metadata" and is fetched by Kobo separately from the book, and you get whatever is cover.jpg showing as the book cover on the device. If you open your book and go back to the cover page, it's probably the image you're expecting to see.
So, my best educated guess would be to change the cover itself in calibre to be the dimensions you want rather than do it in book conversion options. How exactly, I'm not sure, I don't have a calibre install accessible right now and I've never needed to do it.
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