You want to test this stuff as realistically as possible. Changing the amount of fuel means changing launch weight which means (presumably) changes in throttle

You want to test this stuff as realistically as possible. Changing the amount of fuel means changing launch weight which means (presumably) changes in throttle profile etc. The control systems are also probably designed with a certain weight to reach orbit so it's possible that an unusually light rocket would be unstable. I'm not sure whether this would actually make a difference, but if you know it works at nominal fuel weight then you have some confidence it would work during a real launch.