Amazon don't have "their own ISBN". Amazon have something called an ASIN, which, for printed books, happens to be the same as the ISBN. But that doesn't apply to digital books.
As far as I know, Amazon assigns the ASIN when they put the product on sale. The vendor has no control over it. If they are selling books (or any other content) in different formats, they would presumably have different ASINs (just like when they sell clothes in different sizes).
Mike
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