First, you can't- the two ports on that enclose are to enable daisy-chaining. Secondly, even if you could multiplex the ports, the controller that multiplexes PCIe onto TB sits on only four lanes, and even if there was some magic solution to multiplex independent TB controllers into a multiple PCIe link (bearing in mind that none exists because a PCIe "connection" is more than a mere sum of lanes- read the PCIe spec or look at the pinout) the most you'd get is x8 lanes, and not x16 as you say!
I go off information Apple made available- there's no TBv3, and the new MP is limited to 40 lanes of PCIe GEN3, and TBv2 controller is PCIe GEN2 x4- there's no way around that...
How is this relevant to the PCIe/TB discussion? I have no idea what "they" do in After Effects, but perhaps they should "enable" "multi-processor" otherwise they've just wasted money on tech. they don't use and probably suffering from degraded performance... And, in any event, if that really is the case, then I take it as "those guys" are not planning on buying the new MP as that would be a mindless waste of money...