I have a partial answer. It looks like I can duplicate the .uproject file and set the enable flag for the plugin there. For example, I’d have a MyProject.Oculus.uproject and a MyProject.SteamVR.uproject and the only difference is that for the Oculus project I disable the SteamVR plugin. Then I can just pass the correct .uproject to RunUAT.bat.
I still don’t know how to pass preprocessor definitions though.