The 4770K has only 16 lanes of PCIE3 available. When anything is plugged into the 3rd PCIE3 slot, these 16 lanes are split among the slots x8/x4/x4. SLI needs x8 per slot minimum, so what you read is correct -- anything in that third slot, graphics or not, precludes SLI.
The ngff slot uses PCIE2 lanes from the z87 and will not conflict with the GPU. Look among the ROG guides for recent write-ups on ngff cards -- size, keying etc to fit ROG cards.
Jeff