Someone correct me if I'm wrong but I believe the green dot focus confirmation display has anit-flicker built in which limits its accuracy. I find it useless as a manual focus aid. As I see it the only thing it does is tells you the camera "thinks" it's in focus. It might be affected by the AF fine tune default value if set. If a camera is out of calibration the green dot can't be in calibration. It's a phase detection driven display.
I agree with everything but the 'only'. This is no different than AF, the camera might think it is in focus but the proof of the pudding is in whether the image on the sensor is in focus, so the optical path length from mirror to AF sensor and mirror to sensor have to match.
I have the feeling that the AF system has improved considerably over the last couple of years, also improving the reliability of the green dot for manual focus. But it is still the case that one has to practice its use: for fast lenses, there is a considerable interval of focus distances which lead to a dot appearing, the margins of which are marked by a dot-arrow rapid flickering pattern. You have to know for each aperture at which point in that interval the best focus lies. It may be in the middle, but it may also be somewhere close to the edge. The reason for this variability might be the different degrees of correction of spherical aberrations of the lens. With a fast lens, the edges of the 'dot appearing' interval might lead to a badly defocused picture, so it is not enough to simply wait for the dot and shoot.
After some practice, one can use the green dot without looking at it. Peripheral vision is enough to decide the points at which it flickers, and one can focus on composition and what's happening with the subject.
I don't question the ability of some people to focus their lenses through the viewfinder (with the stock screens and without looking at the green dot), and I understand that the Df might be especially well suited to this task, but I don't think it is a viable solution for everyone to achieve a near 100% hit rate with fast lenses. When the light levels are low (dusk and dawn, where f/1.2 is maybe the only aperture that still allows one to shoot at normal ISO levels), my eyes cannot see what is sharp anymore, but the dot usually still works (recent AF sensors have insane sensitivities).