They have to calculate your torque to the rear wheels, and because 4th gear is 1:1, they don't need to calculate the trans gear into the mix.
All they have to do is take into account the rear end gears and tire size, all of which effect rear wheel torque.
Essentially, the dyno reads rear wheel torque, which goes [engine torque * trans gear ratio * rear end ratio * tire ratio = rear wheel torque].
So you will get something in the thousands of ft-lbs of torque with that calc. Then you plug in the known variables (trans, tire, rear wheel torque) which will isolate engine torque, which is not known. So once you have engine torque, you multiply that by .85 or .80, depending if you have a stick or auto, respectively, and that is the torque that the engine alone applies to the rear wheels.
Scott