Up until this point both Intel and Apple have said that TB must have direct access to the GPU and that is was not possible to have a PCIe based TB card for this reason.This seems to solve the question I've had concerning a Mac Pro with a discrete GPU on a expansion card. I guess a new Mac Pro will be able to pipe the graphics back to the motherboard through the TB controller and out the back.. That way you won't need a TB controller on the graphics board itself, or an integrated GPU on the mobo just to guarantee that the Mac Pro have graphics enabled TB even if you change the graphics card.
If the MP has TB on the logic board there should be no problem with the PCIe GPU so long as it is a supported graphics card.
Though TB will be a welcome addition to the MP, if there is one, the real benefit of the MP is the on-the-board PCIe expansion slots. You can, for example add one of the new PCIe SSDs that do not use the SATA interface and are much faster or a PCIe XQD card reader to really speed up the import of large image files without having to buy all the external equipment to hook things up and the overhead of running it through multiple controller chips because it is outside the box. Towers still have value.