It's really a shame that they don't wire both bottom pcie slots for 8x and make somekind of switch or that motherboard recognizes in which slot is second GPU. They had those smart PLX chip implementations already on Z87 boards. If you had 'just' two GPUs it bypassed the PLX and if you had more it was used.
A lot M-ATX cases now have 5 slots and this way you could have two GPUs and another one slot card, or just more space between.
Maybe next gen