I've used OpenGL a very little bit on the three main os, but never that much to run into such FPS differences.
Nvidia on Linux should be as fast as on Windows, X-Plane for ex. runs 20% faster with my GTX770 on Ubuntu.
This is called proof by example.
Game systems are complex. Yours or X-Plane's cases may not stress the same usage scenarios as Alien Isolation does. It could be difference in performance in a feature that has an easy marketed label attachable to it ("oh, it's geometry shaders that are slower", or "oh, tessellation is this much slower") which can be easy to attribute to layman terms, or it might as well not, and it could just be about some internal API call access patterns that a specific engine or a new fancy rendering technique might need to use.
What is causing the actual slowdown in this specific case, your guess is as good as anyone else's, and the only way to know is if you could ask the first-hand developers who have access to the code and have profiled the game on multiple platforms.