Of course videocards can run more fps than the human eye can register. But they can run higher for stability reasons. I don't know the details, but at certain stable fps, the communication between gpu and cpu and in game engines works better in sync and produces different, more pleasable results. For example, running Call of Duty 2 in 125 or 333fps gets the most out of the physics engine, allowing you to jump higher.
And of course videocards don't lock their fps down to the most a human eye can register. Of course you can still do that manually to save gpu usage or to get a stable fps for certain reasons like I said above. High fps in those benchmarks basically allows you to compare the performance of one card to another, one that runs at 90fps give the same experience as one that runs at 180fps, but you can roughly conclude from this that the 180fps card is twice as strong. Thus future proof.