Check into running your GPU on a 1x slot instead of the 16x slot. I have a couple of boards with onboard intel graphics and neither are utilizing the 16x slot available, instead I have used the 1x slots to run GPU's and using the onboard graphics for display. Any time a card is plugged into 16x it disables the onboard.
Using 1x to 16x extenders will allow you to run your gpus in the 1x slot. Even a 1x to 1x extender notched out will allow 16x card to run as well. Give it a shot it has worked just fine in my situation.
It might be possible to just use electrical tape on the unnecessary (greater than 1x) lanes on the card? I havent tried it, but it should work by making the card operate in 1x mode, even though it's placed in the 16x slot.