I think you misunderstand the guidelines. Justification never appears in the body of the book, either in the KF8 file (because it's in the style sheet) nor in the Mobi 7 file (because there is no style sheet, and the in-line styles do not include that instruction). Or perhaps the Support responder misunderstood, which has been known to happen. I have a couple dozen books for sale on Amazon; all have justified text on both the Look Inside sample and (of course) on the actual book delivered to various devices and apps. And none has ever aroused Amazon's ire.
I suspect that most New York publishers also use the text-align instruction, since most of their books are justified on the Look Inside sample.
You're very likely correct that the hyphenation issue is introduced in the publishing process. (It's not the only such issue: the Start Reading Location appears to be set there also, and there's apparently nothing we can do about it.) It could be that Amazon is experimenting with auto-hyphenation. Like you, I wish it wouldn't!
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