Have You compared GTX1060 performance between PCI-E x16 and M.2/x4?
GPU-Z shows x4 3.0 or x4 2.0 operation while connected to the M.2 port throught adapter?
There's lots of articles around that extensively test PCIe lane and gen scaling: https://www.techpowerup.com/reviews/NVIDIA/GTX_980_PCI-Express_Scaling/
Depending on the game and resolution, it's usually a 0-10% drop in performance from 3.0 x16 to 3.0 x4.
GPU-Z shows 3.0 x4.