2-WAY CF/SLI - use PCIEX16_1 and PCIEX16_2
3-WAY CF/SLI - use PCIEX16_1, PCIEX16_2 and PCIEX8_2
The question is Should vs Could - you really wan the bandwidth of the PCIEX16 vs PCIEX8 slots, otherwise it really defeats the whole idea of X16 + X16. The GPU in reality will not go past the X8 bandwidth; even an GTX 480. However, why create an unnecessary bottleneck.
All, I can think of anyway, X58 MOBO PCIE spacing is identical, and most spec SLI/CF GPUs are designed front to back airflow; the non-spec still cool the GPU adequately, but heat the case - so have good {slight negative} airflow and you'll be fine.
Hope that answers your question completely.