It applies to the amount of lanes your CPU (obviously mainboard too) can handle.
5820K = 28 PCIe3.0 Lanes
5930K = 40 PCIe3.0 Lanes
5960X = 40 PCIe3.0 Lanes
E5-2600/4600 V4 = 40 PCIe3.0 Lanes
E5-2600/4600 V5 = 48 PCIe3.0 Lanes
E5-2600/4600 V6 = 48 PCIe3.0 Lanes
6800K = 28 PCIe3.0 Lanes
6850K = 40 PCIe3.0 Lanes
6900K = 40 PCIe3.0 Lanes
6950X = 40 PCIe3.0 Lanes
A GPU uses 16 lanes, two GPU's use 32 lanes, etc.... If you're using a 5820K or 6800K and expecting to run dual gpu x16(2), then you're stuffed.
I agree with your frustration though. The engineers ought to have provided expandability between the PCIe slots and not just limit them in a hierarchal manner. 123456. The lanes ought to change dynamically based on the type of component is added to the slot. It should not matter which slot a PCIe component is installed, as stated previously it ought to change dynamically based on the users needs. OR provide the users the ability to change the PCIe order within the bios. much like we had to do with IRQ's in the long past.
Edited: Updated CPU list
Edited by HIGHPOINT - 6/14/16 at 4:39pm