You are correct, maximum flow is not what is most important. It's more about velocity (from which port energy is derived) and shape. It would be nice to keep the port speeds around 300 fps average, but for a SM/Edelbrock style head on a large cubic inch motor, there is not enough area available to get the speeds that low.
The whole 'see how much flow I can get' thing is just a way to keep the testing interesting. You have to have a goal - something you are trying to achieve. That way you can look back at the end of the day and (sometimes) feel like you accomplished something.
Efficiency is a tough one to quantify. For instance - try to measure valve curtain area and really get it right.....