Yes, because the PCIe root complex in the CPU can only connect one other device besides the southbridge, and that's used for the Thunderbolt controller on the left handside. The second Thunderbolt controller is connected to the southbridge (as are all the other PCIe peripherals), so it doesn't have the same number of PCIe lanes available as the one directly connected to the root complex.

Apple could have solved this by connecting a PCIe switch to the root complex and attaching both Thunderbolt controllers below it, but that would have consumed additional energy. Alternatively they could have used a beefier CPU with more PCIe root ports on the CPU, but I guess those available would have been too energy hungry. Which kind of means this is Intel's fault for not providing a low-energy chip with enough PCIe root ports on the CPU.

I'm wondering what the situation is like on the 15" version with discrete graphics. This would require 3 root ports directly on the CPU to drive both Thunderbolt controllers and the GPU with full speed, I assume that's indeed the case since it's not mentioned in the document.

Another thing not mentioned in the document is that energy consumption will be suboptimal if one device is attached on both sides of the machine because it prevents one of the Thunderbolt controllers from powering down. One should connect both devices on one side to improve battery life.

Edit: On Skylake the PCH is apparently optional, the functionality is mostly integrated into the CPU, so the limitation is really the number of lanes provided by the CPU, and this wasn't sufficient to connect both Thunderbolt controllers with 4x. The CPUs used in the 13" model all have 12 lanes, the ones in the 15" model have 16 lanes. So for the top-of-the-line model this could be 4x for each of the Thunderbolt controllers, 4x for the GPU, 2x for the SSD, 1x for Wifi, 1x for HD Audio?