This person says that BepInEx stopped working from version 1.1.3.
Linux
He also says that it worked fine up until version 1.1.1.
It seems that a solution to the problem has also been proposed.
If you're experiencing the issue, why not take a look at this?
(Is the Unity vulnerability in 1.1.1 really that bad...?)
By the way, I've never had any problems with this mod not working in my environment.