I can answer a few of these questions.
- The Controller opens and closes the Master Valve once per schedule. A note is that if you have Smart Cycle enabled, it will close the Master Valve while it's soaking.
- When a Schedule finishes the Controller shuts off the Zone Valve first, waits 1/4 a second, and then turns off the Master Valve.
Water Hammer prevention works by turning on a Zone before its "official" start time. A quick test that this is happening for you would be to create a Schedule with 2 Zones in it and then manually run the Schedule. You should see both Zones running at the same time when the Schedule is transitioning from the first Zone to the second.
Unfortunately we can't do anything about the water hammer from the first Zone starting.
I hope that clarifies a few things. Let us know what you find!