Try the updated “Batman: Arkham Knight [vorpX]” profile from the cloud. It allows you turn shadows off on the ‘Image’ page of the vorpX menu. Also has a scalable 3D HUD now. I might have missed some related shaders, but worked for me in the first hour or so of the game. Let me know if that changes later.
Additionally I reduced 3D-Strength in EdgePeek mode for comfortable cutscene viewing even if you raise the general 3D-Strength.
BTW: I understand that exaggerated stereo 3D looks cool, but if you keep things real, which is what official profiles do at default, typical non-stereo glitches are often passable. Cranking the stereo 3D-Strength up beyond realistic levels is not always the best idea.