Well, I don't use KindleGen, but upload my epub to the KDP and let it convert there. Though the file is called a "mobi" it actually contains two or three books: a Mobi 7 file for the older Kindles, a KF8 file for the newer ones, and sometimes the file you originally uploaded (depending I think on what that file was). The correct file will be delivered to the purchaser, depending on the device he's downloading to.
Unless altered somehow by your CSS, a hyperlink will show as blue in a Fire tablet but black in the grayscale Kindles.
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