Z97 Extreme4x 16X PCI-E Slots Reserved for GPU's?

It will work fine, the documentation is trying to say that graphics cards are supported fully in those slots. They are capable of supporting a GPU but you can just as easily slot a PCIE x1 soundcard/LAN controller into them without issue. A PCIE x8 RAID controller should be fine and is within the lane specs for the Z97 chipset. Basically the GPU will run at X8 (as intended) and the RAID controller will run at x8 just like if you had a second GPU installed so long as you use the correct PCIE slots (PCIE2 and PCIE5).

Edited by Xaltar - 07 Oct 2015 at 3:53pm

There will be no performance impact on your GPU at x8, in fact there would likely not be any even at x4 with most mid range GPUs. AMD allows for crossfire in an x8 - x4 combo which they do not feel will negatively impact performance to any significant degree. x8 - x8 -x4 triple crossfire setups with high end AMD GPUs see only the smallest of bottleneck vs dual card x8 - x8 scaling and a lot of that bottleneck comes from driver implementation and other factors.