I am with you on each test being the same, they have to be for accurate results. My point is, with no load on the engine, the test standards are so low, both should come out even since it doesn't take much to run on a test stand.
You cannot change anything except the distributors and plug gaps. The timing must be exactly the same, along with the fuel settings. I would suggest using gauge blocks placed between the throttle stop and lever. If the engine runs more or less rpm, you know it's the ignition and not the carb setting. By altering the speed after a change, you alter the parameters of the test. Change block thicknesses for different rpm test, not the set screw. Any change to the carb, no matter how small, fouls the tests. A different rpm only means the engine is performing better or worse on the ignition system, so let the rpm stand where ever it ends up using the same gauge block on both systems. With standard block settings for rpm change, the engine is receiving the same amount of throttle opening, so any difference in fuel usage should come from the ignition. Higher rpm means better mileage, since out on the road you should have to let out of the throttle to run the same speed you was before with more throttle.
And for a fuel system, install a T fitting with two shut off valves coming from two fuel tanks. For the tests, use a clear 1/2 gallon tank with bottom drain and a clear fuel line running to the T fitting. Mark a full line on the tank and empty line half way down the clear fuel line. Use the main tank to get the engine up and running and set, then shut off the main and open the test tank. Start the stop watch when fuel starts flowing, stop it when it hits the empty line on the fuel line. It may only take a quart of fuel, depends on how long you want to watch it run.
It will be interesting what you find. Don't forget to factor in break-in time. The more you run the engine, the looser the cylinders get and the better it runs. So will a newly rebuilt engine gain mileage as it finally seats in all the critical parts, or was it the switch in ignition systems?