Motherboard says PCIe 3.0, but chipset only supports PCIe 2.0. Who's right?

Your CPU has 40 PCIe 3.0 lanes: Intel® Xeon® Processor E5-2620 v4

The communications with your GPUs will be direct from your CPU. This is good, after all the memory controller is also integrated on the CPU meaning that the fastest route for data in memory is from RAM -> CPU -> GPU rather than RAM - CPU -> Chipset -> GPU

The motherboard connects the PCIe connections from the CPU to GPU, but that does not mean that they need to pass through the chipset. They go direct from the CPU to the CPU served PCIe slots.

Somewhere in your motherboard documentation it should tell you if any of the PCIe slots are served by chipset or CPU. Chances are the chipset PCIe lanes are used to serve an m.2 slot or SATA controller. Possibly even USB3 or Gigabit Ethernet. How it is wired up and what to is down to the motherboard designer.

Found your effective chipset/CPU/GPU layout on the Intel page for that chipset: