There are a few more good reasons to run in 4th gear.
1) Power to accelerate a rotating mass (rear wheels, axles, gears, drive shaft, clutch, flywheel, etc) goes in direct proportion to angular acceleration, (i.e., P = Iαω). So the faster you accelerate, the higher the inertial losses in the driveline.
2) In 4th gear, the transmission’s input shaft and output shaft are directly coupled (1:1) so there’s less loss through extra gearing within the transmission.
3) There is less chance of tire slip in a higher gear due to the lower rear-wheel torque.
Other than that, (and assuming you stay under the speed limit), the dyno doesn't much care about the actual gear ratio. It backs that out by monitoring the rotational speed of the drum and the engine speed to give you the right torque numbers. I agree about having a longer pull from the tuning aspect.
I would also like to see the RUNFILEs for dyno runs you guys make! That would be awesome! I haven’t heard of a shop yet that wasn’t willing to give them to the customer. :cheers