I've never seen any difference on epub uploaded to KDP and a downloaded mobi, azw3 or KFX and those produced by Calibre.
I doubt Amazon uses the KindleGen as supplied for PC.
We don't know yet what difference existing epub to kindle via KDP and propsed send-to-kindle will be. Whatever Amazon does with covers or .epub renamed to .png and emailed today may not be the same as the "new" service.
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