Seems very different in each state.
We went through this with Marine Safety Victoria a few years back.
Their opinion was as long as the pilot is appropriately trained and the aircraft was registered under a national body, then that over-rode their requirements. They suggested that a boat licence would be highly regarded however wasn't required. They were happy if we proved that there were an appropriate number of MSV questions in the float-plane rating exam.
As I understand it the Melbourne based Seaplane operator has a Coxwain's certificate from his background, but they told us it wasn't required. Puts him in a good position though in case they change their minds later on.