Well, I've never used KG or KP to create the "mobi"; I upload the epub to the KDP, then download the converted file. I have always stripped out the cover for the KDP version. I have never done anything about the NCX file. The Go To > Cover always works on the preview and in the published book.
The question earlier came up in the KDP forums about the wisdom of including a cover. I argued it made no difference, since the included cover would simply be replaced by a degraded version. My interlocutor argued that it DID make a difference, because it ballooned the size of the book file if a cover were included.
So yesterday I revised a book to include the cover in the uploaded file. Its previous size had been 1259KB. Today it shows as 2110KB. So the interlocutor was right.
Depending on how Amazon slices & dices, the download fee on the first version was about 20 cents. On the new version, it's about 33 cents. On one thousand copies, that's a difference of $130.
I can't think of any reason not to rip out the cover and pocket the $130.
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