It's because the CPU provides PCIE lanes as well as chipset. Because that board supports two gens of processors, 2nd and 3rd, the PCIE standard changed for 3rd gen, and PCIE 3.0 was released. The board's chipset and the 2nd gen processors were both made using the PCIE 2.0 standard, but 3rd gen CPU's offered 16 PCIE lanes.
This will become relevant again soon with the imminent arrival of PCIE 4.0. You will find there are PCIE 3.0 boards with support for PCIE 4.0 processors. Although this diagram isnt PCIE 2.0, it gives you an idea of how both chipset and CPU provide PCIE lanes to a system..