I build off EVGA exclusively for all my SLI rigs, and the PCIe slots aren't any different than other MOBO's standard spread. Keep in mind the GPU itself stripped (w/o coolers) is ~ 1/4" wide, and the cooling is Front->Rear. The non-reference + SLI GPU can still pull the air fine.
However, I must note - the non-reference do a better job cooling the GPU but they also do a nice job heating the case so add a/an large top venting fan(s).
Hope that helps.