This assumes, of course, that the PCIe lanes in question actually exist† and are dedicated to the card, and are not shared with another in-use device via a switch or similar chipset shenanigans.
Case in point: the only time I ever had performance problems with my eGPU setup was when attempting to do 4K HDMI output through a Blackmagic Decklink card while simultaneously using the 1070Ti for compute over the same (shared) Thunderbolt bus in DaVinci Resolve.
As far as I know, this would not typically be a problem with a single-GPU, non-Thunderbolt-connected desktop system, as desktop motherboards typically have at least one full-bandwidth x16 slot, which you'd almost always use for the GPU.
† Physical x16 slots can have fewer than sixteen connected PCIe lanes. For example, while my HP Z820 has four "x16" slots, only three have full bandwidth; the fourth slot supports x16 cards, but only at the speed of an x8 slot, because only eight of the slot's sixteen PCIe lanes are actually connected.