After a lot of testing, I have come to the conclusion that this controller is NOT compatible with indexing valves with its current softwware/firmware combination. This is because the controller will not cycle the water off between zones. I set it up per the instructions, and the water pressure is utterly consistent from the beginning to the end of the schedule. If you think about it logically, there is nothing inherent about having a master valve that would cause the controller to cycle the water off between zones. In fact, if you have a master valve AND zone valves, this would be unwanted behavior.
In addition, the suggestion above for getting it to work with an indexing valve is fatally flawed. Apart from removing the controller's ability to break a zone down into multiple smaller cycles to prevent run-off, etc., this method simply won't work because there is no way of knowing how long the controller will run each schedule, so even with a ½ hour schedule, and one hour spacing between schedules, there is the distinct probability the waterer will run over time, and miss a zone. Of course with an indexing valve, this makes watering akin to Russian roulette.
It does, however seem like it would be fairly trivial to get indexing valves working with the controller. Simply adding another switch to the advanced settings called "indexing valve," and having firmaware on the controller that forced the the water to cycle off for 1-2 minutes between zones would completely solve this issue. But unless and until that happens, this controller will simply not work with an indexing valve.