Apple might go for the solution of having one of the GPUs (whichever gets less performance penalty) in x8 while the other will keep the x16 link, having another x16 for the 3 TB3 controllers and the SSD.
Would be a compromise solution, not ideal of course.
I'd rather have full x16 on both GPUs I guess, it might come useful in the future.
Those 48 lanes in Skylake server parts would be sweet here though, no compromise.
Actually, for me only one TB3 controller and a large SSD would suffice, so the 40 lanes would be enough, but others will need more.
I think with PCIe 3.0 with 8X should be more than enough