Xinerama is totally optional in the X server, and is not used by many applications. Add a USE flag for it in the X server. The catch is that for all ebuilds depending on libXinerama, they'll have to depend on xorg-server with USE=xinerama, but this is really more correct and offers more flexibility.
While I'm all for optional Xinerama support in client applications, I think we'll keep it enabled in the server until it's made irrelevant. For now server-side Xinerama (panoramix) is still used by nvidia-drivers, for example. As for client apps, none of them depend on the server, only on libX11 (or libxcb). Thanks