Enahs, there are major difference between Direct X 9.0 and the current versions of Open GL (1.2~1.4).
Sure, in the end, both APIs push colored triangles but that's like saying that you can compare PERL, C++, and BASIC because in the end, it gets compiled down to machine code. You can't simply take 2 different games with different APIs and compare hardware.
Also, please remember that HL2 is doing a few more things than the Doom 3 Alpha did. That is not because HL2 is better than Doom 3 but because HL2 is going to come out soon and is feature locked and Doom 3 was ONLY an alpha so it wasn't feature locked nor did it show off all its features like the HL2 Benchmark probably does.
Finally, in general, remember that Carmack has programmed many different OpenGL render paths for ALL the particular hardware paths. It suits his style of programming and is the OpenGL way. In DirectX there really isn't the same sort of thing, Direct X boasts its attempt at universally being compatible with hardware. I don't care to argue which API is better but to rather to argue that they are different.