Got my water bill for June/July yesterday and since I have a separate meter for my irrigation, i tried to compare the too.
Iro reported 12,763 gallons used
Bill had 16,000 gallons used
so i assume the difference is due to head precipitation rate.
Is the only fix to do catch cup to measure?
Determine Zone size with Google Maps. Use satellite view, right click, select ‘Measure Distance’, draw your area and Google will tell you the sq footage.
I assume your bill breaks out irrigation? Mine doesn’t, so I can’t quite tell how much I use for my long showers. 
2 meters, 2 separate bills. The only thing fed by the 2nd meter is the irrigation system. You’re billed at a lower rate because the water doesn’t go into a drain to the water treatment plant for processing.
Correct. That’s how I’m setup
Changing square footage is another fix for gallons used.
The catch cup test is really to better dial in the setup for your nozzles.
I ran each zone for 3 minutes. Recorded the gallons used at the water meter and at the Rachio app. Then I programmed a custom nozzle for each zone. Gallons used as recorded by the water meter and the Rachio are withing 2%. No cups required.