It's DirectX 9.0c (Windows) versus DirectX 9.0c -to- DirectX 9.0b-esque OpenGL2.1 (Linux).
At the time of these benchmarks their translation layer didn't support more than DX9.0b, though I believe this was quickly fixed a little later (but we don't have new benchmarks from Valve, although one could do his own!)
I agree it's a mostly worthless comparison of outdated APIs, but to be fair to Valve part of the reason of their excitement was that they started with a port that ran at 6fps and after working on it with the support of all 3 GPU vendors performance became as good as it should have been.