A brake dyno in theory works... however 2 machines will never be calibrated the same. The levels of friction vary to much, and not to mention heating of the friction material causes more inconsistencies. It worked back in the day without computers. Now days a water brake is used instead... however I don't think that could be scaled down to our application. It would be hella cool though

Regarding motor temperatures, I see it as a good point. As it will give you a better understanding of how the motor will behave under heavy load. You wont be making pull after pull as that would be unnecessary. I believe there is enough thermal mass in the motor, wires, heat sinks and a solid metal frame to make this negligible.