before you get too hung up about sacrificing GPU bandwidth by putting the NIC in the 2nd x16 slot and droppinbg the GPU from x16 to x8, check the specs on your GPU - you'll be surprised how many GPUs actually only run x8 anyway!!!
On the server end things are even easier as typically all you want is a text mode console, - that's where open ended x1 slots come into their own, lots of the servers at work have the console gpu ( typically a low power card like a quadro 600 ) in the pcie2x1 slot -works fine and maximises available high bandwidth slots for cards that actually need it (raid controllers , high speed NICs, computer oriented GPUs etc). See attached photo of an old z420 we use for testing stuff at work - the top gpu ( in pcie2x1 slot ) is running the console, all the rest as passed thru in esxi to vms ( yes, we had to raid the deepest parts of our 'junk' gpu box for the test to find enough single-width gpus ). Helps that the z series has a BIOS setting which allows you to explicitly select which slot will be use for BIOS POST/console.