So here are some initial observations…
I hate adjustable anything when it comes to irrigation. You have no idea how much water you are actually putting out. Those 1300’s can range from 1.0gpm to 2.3gpm. Part of why you are getting so much runoff when Rachio in command is that it is currently set for 1" per our PR, but even at their lowest flow, those bubblers are putting out WAAAAYYYY more than 1"/hour. I need to sit down and do the calculations on it to figure out what it actually is…even with you only running for 3 minutes at a time, you are might be putting down in excess of 6.9gpm
Based on the soil in your area, I’d say that you setting should be set to sandy loam, or hell, maybe even sand. The predominant soil is that Myoma, which looks like it soaks water extremely fast and can be in upwards of 36" deep, so I’m interested as to how you are seeing ponding. Was outside fill dirt brought in for the landscaping by chance?
All in all, your system is not set up ideally, but we can make some concessions and get it dialed in so that it will “work”. You have a big mix of plants with vastly different watering needs, and utilizing adjustable bubblers, some feed a single plant, others feeding multiple.
I think we need to first reset everything back to default settings and start over. From there, I think we need to look at your soil type and confirm what exactly the Myoma falls into. Looks like it is about a .7-1.1 AW, which falls into Loamy Sand and Sandy Loam. Lets set it to Loamy Sand (.7 AW) to play it safe. I’d probably cut the root depth back to 15", and we need to calculate the Inches Per Hour on those bubblers.
Sound like a good start?