Even if Mesa is configured to be built with "d3d9" and "gallium" USE flags, it will skip building Gallium-Nine libraries if no supported drivers are requested (e.g. if only "video_cards_intel" are set). Therefore wine-any (and probably other Wine flavours also) configured with "d3d9" will pass Emerge checks for USE constrains, but fail at configure time saying "configure: error: pkg-config couldn't find Gallium Nine module".
Workaround for this is to enable excess driver in mesa that supports Gallium Nine (e.g. video_cards_nouveau), but I think it's better to extend USE checks in wine ebuild (with "one-of").