I completely nuked the Installation Folder, Set the compatibility to Proton Experimental, then reinstalled the game on my OS Install drive, and so far so good. haven't played enough to see how performance does, but rather than running native this fixes the graphical bugs that I have had so far.

This worked for me, I'm not sure if this is going to 100% work for anyone else, I had a hard time getting Black Mesa to start in compatibility mode when it was already installed on my system.