Having an accurate zone area is pretty important if you want everything to line up. The calculated PR depends on the area of the zone, by using 1000 as a default you're not going to get an accurate PR and thus the watering time will not be optimized by the Rachio algorithm. You don't need to be exact but walking your yard with a tape measure and visualizing squares/triangles/circles (easy area calculations) will get you closer than just using 1000. Rachio defaults to 1000, however, they’re using an average PR for the type of head that you select which is assumed to be relatively close so the derived zone run time should be in the ballpark. If you’re using 1000 for the PR calculation and then significantly changing PR values when creating custom heads your zone run times cannot be accurately calculated by Rachio. At the end of the day your lawn will still get good water, PR is not the only factor Rachio uses to determine run times but it is a player.
An accurate SF measurement is probably most important for getting the app to show your exact water usage. Your actual water usage will likely be way different than what Rachio says you used or saved. I believe the app calculates your water usage using the PR, the area of the zone and the time that the zone runs. If you get accurate zone areas you can get your water meter to be very close to the numbers the app spits out (Rachio says my July usage thus far is 3993 gallons, my water meter reads 3926 gallons - close enough for me).
One more thing I've learned when using this method and trying to be as accurate as possible: you need to be cognizant of what's happening to your pressure when you're watering. If you measured your flowrates when nothing else in your house was on but three people are showering when your system is watering your flowrates will be off. Similarly, if you did your testing at noon when no one is watering but all of your neighbors water at the same time you do your numbers will be off. I water at 1:00 AM because I found that's when the least number of people near me water (maximize my pressure) and my cycles are complete before anyone is awake and starts to use water in the house. Ideally you should take your measurements when your system will normally run. Just something to keep in mind....
I think you should take a look at a higher level and make a determination how important it is. My yard is about 1800 SF total, however, I have 7 zones. If I used the default 1000 with average PR for heads the watering times would be fine but the usage data would be off by a factor of 3.9 (7000/1800) which is way too much for me. It looks like you have 16 zones, if your yard is near 16000 SF total, everything will probably be close; if it’s significantly bigger or smaller accurate zone areas are important.
For what it’s worth I think if you’re going to use the 1000 default setting you should just stick with the default PR values and not even worry about creating custom nozzles.
Hope that helps!