I've asked about this and the general opinion seems to be that the scope rail should be left on as it stiffens the action.
Dave Ramshead still has his scope rail on and he does okay with his when he uses it.
I did okay at the Gathering (57) and I'm hardly a masterclass in shooting.
I heard some people have had their rails skimmed to take a bit off, although I'm not sure how that'd be done.
I've got some BKL 30mm low mounts on mine so while it's higher than usual it's not that much higher and I'm getting used to the close up aim-points.
I love my PT, mine's the short action. It may not be the perfect HFT rifle scope height wise but it just feels so nice in the hand...