I used to follow the threads about this problem extensively. I never had the problem myself, but I was curious about it.
Anyway, the fan problem has nothing to do with the source of the EFI (or lack of EFI) in the video card. This was evidenced by the fact that it also occurs for some people using official Mac Edition cards from EVGA, and more importantly, even for people with official Apple 5870 video cards. There was another thread where someone claimed to have discovered that it was a bug in the SMC firmware. If true, the problem will probably never be fixed.
I seem to recall that by far most people had the problem with 2009 MP. I cannot remember if anyone experienced it with a 2010. The 2009 and the 2010 do have different SMC firmware.
If the problem occurs, there are two workarounds: (A) putting it in slot 2 instead of 1, and (B) after bootup, run anything that "works" the card by using GPU accelerated effects, such as the aforementioned CUDA Z.
I've always wondered though, with more and more GPU accelerated effects for certain features in the OS X desktop itself, if a simpler (B) solution exists simply by activating one of those OS X features? Can't test this myself as I don't have the problem.