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From what I gather, the page-template.xpgt will override anything in the CSS stylesheet.
I don't know much about the page-template.xpgt, my early experience was that it never made the book look better and sometimes made it look a lot worse, so I always strip it using the Modify ePub plugin at the same time I strip all the other useless crap like DRM tags, iTunes files, Javascript, etc.
It might be possible to make a patch so that the styles in the page-template.xpgt are ignored, but I would have to learn more about it first.
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