Ha! I did some searching last night and found the same PDF. It was very helpful. It’s pretty easy in the end and I don’t want to scare everyone away with a long math lesson, so the short story is this:

Buy some catch cups that capture 16 square inches. (That is a standard catch cup size and that’s what the Orbit catch cups that I linked to are.)

Set them out, run your sprinklers for 10 minutes.

Find the average mL reading across your catch cups. (If you put out 10 cups, add the readings from them together and divide by 10.)

Multiply your average mL reading by 0.0225. The answer will be your nozzle’s inches per hour for that zone. (The answer that you get should be somewhere between 0 and 2.5. If it isn’t, you probably did something wrong.)

Edit your zone and set a custom nozzle for that amount.

You’re done. Move on to the next zone and repeat the process. (Remember to recreate your watering schedules, as a change to the custom nozzle setting does not impact previously created watering schedules.)
Example:
My average mL after a 10 minute run was 53 mL.
53 * 0.0225 = 1.1925
I rounded it off and set my custom nozzle to 1.2.
For those that want the long story, here you go: (If anyone finds an error in my assumptions or math, please let me know.)
It doesn’t matter how many sprinkler heads you have. It doesn’t matter the square footage of your zone. The only thing that matters is the amount of “inches per hour” of water that you put down. You need to figure this out, and set your nozzle for that zone to that rate.
Now for some math:
My average mL collected by my catch cups was 53mL over 10 minutes. I need to multiply by 6 to get that number to represent an hour.
53 mL * 6 = 318mL per hour
But that 318 mL per hour is what was collected across a 16 square inch catch cup. I need to know how much fell in a single square inch. This is referred to in the PDF as the “Irrigation Amount.”
Irrigation Amount = 318 mL / 16 square inches = 19.875 ml/sq inches
But the Rachio software doesn’t want to know this data in mL’s…it wants it in terms of (vertical) inches of water. According to this article, we can convert from mL to inches by multiplying by 0.06.
53 mL * 6 = 318mL per hour
1.2 inches sounds like a reasonable answer, as I see the preset Rachio nozzles tend to range between 1 and 2 inches. If I got an answer like 45, I would have to assume that I did something wrong. Now, I go back into my zone and change the nozzle to a custom nozzle with the value of 1.2 inches. After that, I create a new watering schedule (as changing the nozzle amount won’t impact previously created watering schedules), and the Rachio software will automatically set the correct runtime.
Now that it’s all explained, let’s combine the variable into a simple equation that can be used for the other zones. Assuming a 10 minute catch test and standard size 16 square inch catch cups:
The overall multiplier = 6 /16 * 0.06 = 0.0225
Now, I know that I can take the average mL picked up in 10 minutes in my catch cups, and multiple that number by 0.0225 to get my inches per hour. Let’s try:
53 mL * 0.0225 = 1.1925
And the math checks out!