You can hook up the start relay to the M terminal and enable pump setting within Rachio. You will need to use pump setting to set 2 minute delay between zones in order for your index valve to cycle to the next zone.
More on the delay setting here:
You can keep zones 1 through 4 terminals disconnected on your new controller (they will be controlled via M terminal). Keep in mind that you will need to match all of the zone settings in order to use smarter flex schedules. With index valve you need to make sure that when one zone will require water, all of the other zones will require the same amount, otherwise you run into the risk of system going out of sync with your index valve and leaving some of the zones under-watered while others flooded.