I believe Calibre does some "CSS flattening" step in conversions, maybe you can convert your ePUB to ePUB (or something else) with Calibre, making sure the CSS is processed and flattened, and then convert to mobi with KindleGen or whatever.
Quote:
I know I could use Calibre to convert, but given that I have handcoded my precious epub, I want a bit more control over the behind-the-scenes code than Calibre will allow 
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But I'm sure Calibre allows more control than KindleGen...