Correct, as @Dlane points out. The times are the earliest they will run. In your specific example, if both zones run on the same day, your trees will run from 5-6am, and your shrubs would then run from 6-8am.
I’m not sure where you saw that. If you did I would venture to say it was a minority opinion. What is definitely true is that it takes a bigger investment of your time to set it up. I’ve had my trees and shrubs on drip for about 1.5 years, so I’m going through my second AZ summer now. Without touching anything I go from watering shrubs from every 4-5 days in the peak of summer, to once a month this last January (thanks in part to rain, but also due to cooler temps).
The drip emitter calculator points you to a ‘Water Use It Wisely’ site, which gives you very specific targets for how deeply and how often to water. Once you take your 1st shot at setting it up compare what your Fixed schedule is planning against those recommendations. The ‘Water Use It Wisely’ recommendations work, and they lead to deeper, less frequent watering. If your vegetation isn’t used to that yet you might have to make incremental adjustments until you get to the cycles they recommend.