Rachio does not have a controller more than 16 stations. You certainly can use multiple controllers. They do not interact with each other though. This means that if you do not have sufficient pressure to run two zones, you may have to do some finagling so the schedules do not overlap.
The connections to Common on Rachio are all the same common. It has multiple places for Common just for convenience if needed. In other words, it lowers the need to wire nut a few commons together or try to get them all under a terminal. The caveat with more than one controller is the common for the zones being controlled must be on the same controller.