Linux ATI drivers are better and therefore Open GL performance is better than Windows
Unfortunately, that doesn't address the issues that I have with running Civ V at high res and detail. However, the link you provide shows open source driver running slower than ATI driver. So I am about to ditch the recommended xserver-xorg-video-ati. Your earlier claim that it was a problem with WINE proved incorrect. The game still runs with WINE uninstalled!
Also Ars Technica ran some comparisons between Steam games on Linux versus Windows and found that they ran slower on Linux. The reviewer attributed this to Open GL.