No, it's native Linux with native Vulkan as well.

The Linux version of cs:go had native logic and wrapped rendering via valve's ToGL from before proton. CS2 is fully native though.

This is far from a black and white answer. A lot of the first gen steam machine 'ports', including those from Valve, Aspyr, Feral and Virtual Programming used source code level wrapper libraries to convert D3D calls to OpenGL. This added a little bit of extra overhead to the port so a lot of these early ports suffered a little slower performance (in my opinion an average of about 15% slower). These ports were compiled from source code so they were still native ports, if a little half-assed for time and manpower's sake. As time went on Valve and VP's wrappers improved to the point that you could get 1:1 performance or sometimes much better performance running the port under linux (for example VP's wrapper would multi-thread the renderer even if the original D3D renderer was singled-threaded). Feral went on to re-code a handful of their later ports from D3D to Vulkan, again, achieving better performance under linux. A few game engines were written with linux in mind from the start, such as The Talos Principle/Serious Sam 3, and those titles, in my opinion, would be best to use to compare the relative performance of the two OS's at that time.

Nowadays you still have a fair amount of indie titles coming out with native linux support. Not many larger titles in recent years, but you do still get some such as Psychonauts 2 and stuff from Paradox. Proton has gotten so good now that many games will run better on linux from day 1 than on Windows-steal-yo-data-11.