GTX1080 PCIe Scaling @ Techpowerup
TPU has put up a new PCIe scaling article with a GTX1080, which is relevant to us in eGPU-land.
1) Of note is the "x4 3.0 via Chipset" result, as this is similar to a modern laptop's Gen3, 4-lane M.2 slot. The impact is very small, so M.2 solutions are very good options, assuming the Code 43 issue gets resolved at some point.
2) Thunderbolt results will be slightly under the results reported here, due to the extra latency added by the TB controller.
3) Contrasting this with the GTX980 PCIe scaling article, it seems reasonable to assume that the more powerful GTX1080 card is hit more severely by the reduction in PCIe lanes compared to the previous generation GTX980. But other factors may be in play (driver version, for example). In either case, the change is not large, numbering in the single-digit percentage points from the full width slot performance, which is good news for powerful eGPU implementations on Thunderbolt3 or Gen3 M.2.
4) The higher the resolution, the lower the performance impact. Likely since a lower frame-rate leads to less traffic across the PCIe link. Somewhat ironically, this means you are better off aiming for 4K@60hz, than 1440p@144hz, or 1080p at ultra-high refresh rates (like 180hz or 200hz) on the newest monitors, if you wish to reduce the hit from the lower PCIe bandwidth.
"Always listen to experts. They'll tell you what can't be done, and why. Then do it."- Robert A. Heinlein, "Time Enough for Love."
Also, reddit user /u/mm_5687 summarized this and approximated the impact of 2 PCIe lane Thunderbolt 3 options we're seeing in some laptops (e.g. XPS 15).
Source Testing (which we can easily do ourselves using a piece of tape)
And here's a useful Technical Brief (PDF) detailing TB3's different configurations, DP + PCIe lanes, and how it prioritizes bandwidth.