The cover in the ebook file is completely independent of the picture you give to Amazon and displayed on the product page. The thumbnail you get on the Kindle is automatically generated (since it's grayscale on an e-ink) from the picture on the product page.
The thumbnail shows in cover view, and the book cover in the ebook file will be the first "page" of the book.
I know this because lots of big six publications have horrible generic covers inside the book, but the thumbnails are always from the product page.
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