An unasked for update:
So I learned all about polishing books. Actually I just learned to select something about modifying the cover, so now I have a lot of "original" Epubs. I didn't have to use the resize cover plugin.
I made a list of all books on my Kobo with improper covers (too small and at the top and center, stuck in the left corner, just text, all white or all black) and fixed them in Calibre. Then I deleted them from the Kobo and re-sent them. Given the number of books, it took a long time.
All were fixed except the all-white and all-black covers. The all-white ones were DRM fixed. I could read them on Calibre but could not modify them. I just replaced those. The ones with black covers apparently had an Adobe Digital Editions issue. There were only three of them. Calibre couldn't send them to the Kobo in the form of a Kepub because it said my machine was not registered with ADE. I guess I need to tackle that later.
This was less of an issue before since I used to transfer books as Epubs and not Kepubs. Kobo tends to use the metadata cover for Epubs, and the first page for Kepubs.
I've essentially corrected the covers for all Epubs in my Calibre library. (The large majority of those books are Epubs. There's just a few PDFs that are pointless to convert to Epubs.)
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