The master valve is designed to turn on for each and every run as in a traditional way.
So when you irrigate from the pond, you'd need the master valve to turn on the pump. But when you fill up the pool, you don't want to turn on the pump. With a traditional controller, you'd need 2 controllers to do these 2 different tasks. But it sounds like what you want may be just the ability to specify which run or program should use the master valve. Correct?