Thank you Gene and MeterManSays! I contacted Rachio support and they confirmed the same (i.e. current system only supports 1 flow meter and I need to install another Rachio controller to get 2 flow meters working).
The alternate solution of using 2 controllers does not look so interesting. I guess this is only a software limitation and can probably be supported in a newer software version! (Rachio, I hope you are looking at this!!)
In the meanwhile, if anyone found an alternate solution, i.e. setting up in parallel or using an inexpensive signal combiner, please share!!