The number is not relevant, just the amount the indicator moved from zero. The indicator moved counter clockwise to .060". I guess he was pushing down on the shaft which is why the indicator went backwards.
Yes I set the trans on the tail shaft on the floor then put the dial indicator on and set it to zero as I lifted the trans the dial went to the left counter clockwise to 60 and from zero that =.040 now if you put the dial on while the trans has the shaft in the air and you set the dial to zero it will go clockwise and in my case it would have gone to the 40 =.040