Agreed. Slight difference, probably not enough to notice. Think it out logically, ssuming that you're using only a single card:
PCIe x16 v 3.0 has enough bandwidth for two GTX 1080s and each one runs in x8 mode. So - each card gets 1/2 the bandwidth of a PCIe x16 3.0 slot.
PCIe x16 v 2.0 has half the bandwidth of v3.0. You're not running SLI, so the card runs in x16 mode.
Since a GTX 1080 can run then in x8 v3, the x16 v2 is equivalent in bandwidth, so the slot won't bottleneck the card in any appreciable way.