If the rain sensor input worked as suggested, the EZFlora would be inhibited by default as soon as the rain sensor is enabled until a rain sensor is connected. Not the way it works.
The rain sensor input has to be “pulled UP to inhibit” (see the EZFlora command reference where pin connections are explained) which means connecting the rain sensor input to +5v through a pullup resister to inhibit. When that is done and the rain sensor is enabled the Configuration Register will show the EZFlora Inhibited.
Have not tried it but I guess a pullup resister could be installed between +5v and the rain sensor input with the NC contact providing GND to the rain sensor input. That would in theory have the EZFlora not inhibited while the NC contact is closed. When it rains and the NC contact opens, the pullup resister connected between +5v and the rain sensor input would inhibit the EZFlora.
Seems much simpler to connect the rain sensor NC between the EZFlora and the common valve run. When it rains the NC opens removing one side of the 24v AC. That way no special commands have to be issued through Indigo.
The Rain Sensor Enabled command should be permanent until a factory reset is done. It did not have an effect because the rain sensor input was not pulled UP with a resister between +5v and the rain sensor input to inhibit the EZFlora