ADE has no idea what those amzn media queries are. So I doubt it knows how to even interpret not amzn-mobi. But I can't say for sure.
That's why I use the @import method and use three completely separate CSS files: one for ePub, and one each for MOBI and KF8. That way, I just comment out or delete the amzn-* lines to publish the ePub or vice-versa for building the MOBI.