Taking the Master Value out of the equation for a moment, you should be fine using one rain sensor and connecting all the commons together.
The transformers powering the controllers should be electrically isolating the controllers from everything else. When you have two isolated electrical circits, you're always safe attatching a single wire from any point of circuit #1 to any point on circuit #2. The reason this is safe is because electrical current must flow in a loop. When there is only one connection point, no current can flow.
Now in the real world, you usally can not just randomly touch random points of two circuits together because most electrical circuits are not isolated. Usually some part of the circuit is grounded. When that is the case, ground acts as the return path to compete a loop and nasty electrical things happen. This sort of explains why birds are not hurt when they land on a live electrical wire. There is only one connection point between the bird and the wire... his foot. There's no way for any electricity to flow from the wire to the bird and therefore he remains safe.
Now when you throw the master valve into the equation, you begin connecting the two systems at more than one point, current can flow, and things can get damaged. It would take some sort of a relay controlling circuit to allow the master valve to be fired from either controller. I'm afraid you are going to have to either purchase a larger controller, disable the master valve, or get someone to build you the nessesary relay circuit.