I know this is an old post but:
Well that's me screwed over then, I have an Rampage V Edition 10 running an Aorus GTX1080 Ti Extreme, an Samsung 960 EVO 1G, A Avago 9361-8i Raid controller and an Mellenox Connect X 2 10Gb SFP and the lack of bifurcation explains a lot.
The VGA Card is in PCIeX16_1, PCIeX16_2 is blocked by the VGA ( large heatsync ), PCIeX16_3 contains the Raid controller and PCIeX16_4 the 10G SFP. The problem is the video card runs at X8 when it should run at x16, the only way to fix this is to go into bios and select 4 Way configuration and change it from Auto to X16,x8,x8,x8 - when you do this it disables the M.2 slot but the VGA card runs x16, I also tried disabling PCIeX16_2 using in the on board switch but it is so dumb that it still continues with the lanes in the same config with the M.2 disabled, honestly how difficult can it be to look at each slot, see what is in it and only if it exceeds the number of lanes on my 40 lane CPU drop something to x8 or alternately give me the ability to manually control which slots get how many lanes. Pathetic. I don't have that problem with my X399 board running threadripper. All manufacturers need to give us power users closer to bare metal control over these things we didn't buy boards this expensive because we need our hands to be held.