Alright, this is a very old question. I found the answer in Intel C600 Series Chipset Datasheet, Section 5.3.
The PCH contains up to 8 PCI Express* root ports and one uplink port. All versions of
the PCH contain the 8 root ports. The Intel® C606, C608 Chipset SKUs contain a x4
uplink port while the Intel® C602, C602J, C604 Chipset and Intel® X79 Express Chipset
SKUs do not. The purpose of the uplink port is to provide a direct path for the SAS
controllers, SGPIO used by the SAS controllers, and SMBus ports to the processor/
memory without having to be multiplexed onto the DMI bus and sharing bandwidth
with the rest of the component. The uplink port is not connected to the downstream
So the PCIe uplink is not used by the PCIe slots connected to the PCH, instead, they are used by SAS SCU and extra SMBus on C606 or C608 chipset. The answer is clear, PCIe slots provided by any C60X PCH will never support Gen3.
Motherboards using C606 or C608 chipset are what SuperMicro calls some SKUs. For example, X9DRi-F and X9DR3-f share the same design, but the "i" model uses C602 while the "3" model uses C606.