Your old index valve does not have an off setting, whenever the water is provided, it will go somewhere. The valve in question allowed the index valve to be turned off and the hose to get the full pressure from the pump.
Your new valves, on the other hand, are off by default. If you turn on the hose while one of the zones is running, than pressure / flow will be shared between the two zones, each getting reduced flow.
You can create a third zone within Rachio, one that is not connected to any valve, running that zone while hose is open will provide full pressure to the hose, same as if the old manual valve was closed.