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The amazon media queries (including amzn-mobi) most certainly affect the mobi-only portion of the dual-format file that kindlegen/kindlepreviewer produces. If used correctly, they allow the ebook creator to provide separate css to be used when creating the two formats (mobi/KF8). I do it all the time. I use them in conjunction with "display: none" to make sure the correctly formatted html is displayed/hidden based on the format being generated.
I would guess that if your amzn-mobi supplied css appears to be having no affect on the mobi-only portion produced, then you must be supplying css that is unsupported for the purposes of creating the older mobi format.
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