I've been fine tuning my lenses with the D5 using the automated feature. It seems very reproducible (STD about 1) between instances of repeated LV focus + AFFT operations with the same lens and focal length. However, my 24-70E and 70-200/2.8II give about ten points different readings at the short and long focal lengths, so a compromise value needs to be set. I recommend repeating the auto fine tuning several times and using the average as a working starting point for the fine tune value. I find it seems to work quite well and haven't had to adjust these values based on real world shooting so far.
My test conditions have been using the Lens Align target (larger than normal version target, added on top), about 50x focal length shooting distance, window light indoors during the day, to make sure shot noise doesn't affect the result too much.
I find the AFFT feature is very helpful.
In particular, my 300/4 PF with TC-14E III and TC-20E III required significant fine tuning (7 and 13, respectively) whereas the bare lens is close to zero.