Square footage only affects the calculations of how much water you used (after the fact). It does nothing in calculating how much water is going to be applied.
As far as nozzles types go, as I understand it the ones that are set up are what are the "normal" flows for each type of nozzle. You can get more accurate estimates of your own particular system by doing a catch cup test. I kinda like the catch cup test because with that you can also get an Efficiency % for that particular zone. Using the flow meter or street water meter, you'll get the rate, but not the efficiency. Doing both would probably get you a little more accurate.