Regarding the PCIe 3.0 spec on x79.
The SB-E has 40 primary PCIe lanes, 32 lanes of PCIe 3.0 are dedicated to the GPU(s), all LGA 2011 CPUs & MOBO's are capable of PCIe 3.0, some BIOS upgrades have addressed PCIe 3.0 issues, but the X79 Chipset is a controller for 6 SATA ports (2xSATA3 & 4xSATA2) and USB 2.0 14 ports using an additional separate 8 lanes of PCIe 2.0. Ditto the Z77 has the same 8 lanes of PCIe 2.0. Meaning, the IB (Ivy Bridge) is the second set of CPU's from Intel to run PCIe 3.0 to the GPU(s). All LGA 1155 including the IB have half the number of PCIe lanes to the GPU in comparison to LGA 2011; SB/LGA 1155 16 lanes of PCIe 2.0, IB/LGA 1155 16 lanes of PCIe 3.0 vs SB-E/IB-E/LGA 2011 32 lanes of PCIe 3.0 to the GPUs then split in various ways.
You are confusing a Chipset with GPU lanes. Before with LGA 1156 e.g. P55 and LGA 1366 e.g. X58 the GPU(s) ran through the Chipset, but since Sandy Bridge LGA 1155 and Sandy Bridge Extreme LGA 2011 all GPU lanes are a direct path to the CPU to reduce 'latency.'
Therefore, the SB-E running e.g. GTX 600 series or HD 7000 series GPU(s) is PCIe 3.0 clean *IF the drivers allow it. The problem is with nVidia, the SB-E & AMD HD 7000 series runs PCIe 3.0 just fine. Yes, I've seen this ->
http://www.geforce.com/hardware/de [...] ifications
*GeForce GTX 680 supports PCI Express 3.0. The Intel X79/SNB-E PCI Express 2.0 platform is only currently supported up to 5GT/s (PCIE 2.0) bus speeds even though some motherboard manufacturers have enabled higher 8GT/s speeds.
BTW - Registry fix (hack) to force the GTX 680 to run in PCIe 3.0 mode; see -
http://tinyurl.com/7awc9lv (RMPcieLinkSpeed, DWORD = 0004, etc. IMO - It's a bad act by nVidia...to Disable, if this is an issue on some LGA 2011 then the driver installer 'should' detect and notify the end user to rectify vs all LGA 2011 suffer from the few LGA 2011 with a BIOS issue.
Problem this might be ditto with the IB, since there's no difference in the PCIe 3.0 spec on either the SB-E or IB. The HD 7000 series does run in PCIe 3.0 mode on LGA 2011.
On my end, I'm going to be doing some reading as I will be getting the Sabertooth x79.