I think you are Misunderstanding the Specs. The Maximus II Formula supports PCEe Version 2.0 on all PCie slots. 2 of the 3 slots support PCIe 2.0 at 16 lanes each. Those 2 slots are reconfigured by the system to support PCIe 2.0 at 8 lanes each (dual) when two 16 lane cards are used at the same time, one in each slot. The third PCIe slot is physically wired to use only 4 lanes, however it is still a PCIe version 2.0 slot. The reason is because the Intel p55 chipset only supports 20 lanes of PCIe version 2.0.
I suggest you take a look at the following article for more info. on how PCIe works: http://en.wikipedia.org/wiki/PCI_Express