Did you follow that guide exactly? I would avoid all the gameworks settings if you haven't already.
Could just be due to you running it on a mech. HDD though.
My game isn't perfect but it is fairly smooth overall and the batmobile parts were good too, definitely didn't get any 1-2 second pauses except for when I first load into the game.
I tried disabling Gameworks and it reduced framerate fluctiations a bit but the first batmobile section was still stuttering biblically. Anyways, I've installed the game on my ssd and I'll probably tinker with it tomorrow, maybe I missed something.
EDIT: Or maybe it is indeed impossible to run this off a HDD;p