As for enough PCI-E lanes in PCI-E 3.0 there should be enough since ThunderBolt uses 4 lanes of PCI-E 2.0 and
What is discounted here is the current Mac Pro is oversubscribed on the 4 PCI-e slots. TB effectively adds another slot of pressure. The E5's expand the number of lanes but only out to 40 (***)
16 , 16 , 4 , 4 ====> 40 lanes. ( there are not "extras" )
If throw TB on top.
16, 16 , 4 , 4 , 4(TB) ===> 44 lanes.
They could go back to over committing on the on the last slot. If there is a version 3-to-2 expander switch could go
16 , 16, 4 , 4(v2) , 4 (v2 TB) ===> 40 lanes
The quirky part is how do you hook up the display port output from the GPU if it is on a discrete card. There is a reasonable chance Apple will punt on this until there is a better embedded solution for this in a Mac Pro.
As for the current generation of graphics cards they don't use the full bandwidth of PCI-E 2.0
As purely video cards yes (most of the time). As GPGPU engines no. There is exceedingly little reason to handicap the GPGPU market potential of a Mac Pro. That market tends not to have problems paying for a $2,499+ box.
So there should be enough space for up to 4 ThunderBolt ports on the card itself, but as for this it all depends on how Apple implement ThunderBolt in the Mac Pro
The problem is the TB controller can only drive two physical ports. You'd need two controllers for 4. In the chart here just divide by 2 to see how many video channels you get.
http://arstechnica.com/gadgets/news...lt-controller-could-broaden-reach-of-spec.ars
There are no 4 video ( 8 TB channel ) controllers. You might get two TB ports and two
real DP v1.2 ports for four of the same physical form factor but it would not be 4 electric TB ports. More than two TB ports is a bit of overkill anyway with daisy chaining. (e.g., the current Mac Pro has two Firewire (rear) and two 1Gb Ethernet ports.) Not sure why TB needs, or even wants, a flatter tree.
With two controllers you are up to 8x PCI-e lanes of consumption. It is already oversubscribed with one.
Nevermind, that the graphics card is a flawed place to put a TB controller. Additionally, most users are going to be using non-Apple monitors for the normal, mainstream connectors should be present on the card. ( IMHO they all so be normal, mainstream connectors. There isn't a good reason to lock the card into the Mac market. )
(***) With two E5's there are 80 lanes. At that point there are "more than enough" lanes for lots of stuff (e.g., 4 16x electrical slots ). However, that isn't an option for single socket set-ups.