Apple would have to use an Intel board with dual PCIe controllers. There's no other way to get enough PCIe lanes to support Thunderbolt, which takes eight lanes on its own. There are boards from a couple manufacturers out there that have dual PCIe controllers onboard, but none of the boards have Thunderbolt AFAIK.
Not sure what your on about there?
The CPUs have a fixed number of PCI-E lanes (40ish IIRC).
Two x16s and two x4s kind of use all that up, sharing bandwidth is easy and far from an ideal solution.
Nor does it solve how to integrate display port into it. Either thunderbolt is on the GPU and shares the GPUs PCI-E lanes, or display port signals are send back via the PCI-e lanes to the thunderbolt controller or an external cable merges a non-DP enabled TB port with the GPUs DP port.
Or a discrete GPU is included on the motherboard itself, but then you need to pipe the output from the high performance GPU.
Very interested anyhow on how apple will manage it.