Yes stock are turned off, so the command to disable AnKor's shaders is removed, as there would then be no shaders working properly and it would look a mess.
If you want to fly without AnKor's shadows (say you are mad or your PC can't run them) then choose Default Shaders from workshop before flying.
Thanks Pol, though I can not think of ANY reason I would want to play without Ankor's wonderful shaders!!