I use two fliggtcontrollers in my amphibious rover. One for “rover mode”, one for “boat mode”. The problem I see for your vehicle, is to divide the controls/motors between the two “modes”. Perhaps you could use a water rudder and multiple motors to have two vehicles in one.
Changing between the two modes in a auto mission might also be interesting. It works with my rover, but both modes are equally slow and it does not fall out of the sky if something goes wrong.