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Presumably when I uploaded the kindle genned version Amazon's processing compressed the thing. I would think when someone buys a kindle eBook they would want it to work, no matter which Kindle device they have. I would be worried that stripping out a version would mean that it might not work on one or the other.
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Amazon is only sending you the portion that your device can/will support. Fires (and some apps) are getting the KF8 version... all others are getting the older mobi version. Nobody's getting the entire master/combo version of the file delivered to them. Hence the size differences.
People have been stripping the source portion of the kindlegen output before uploading to Amazon for a long time with no adverse effects, but like you mentioned... I wouldn't suggest stripping out one
format or the other before uploading. You may be limiting someone's ability to view your book that way (it would be different if you wanted to distribute your ebook on your own, and are only concerned with one format or the other).