As I understand it you will place your Yamaha on the foredeck and run an extension cord from its 3 prong outlet to your appliances, right?
That 3 prong outlet has one terminal for hot, one for neutral and one for ground. The neutral and grounds are tied together internally in the generator. When you connect your appliances those three terminals are connected to the appliance as well. So the appliance is case is connected to the ground.
If there is a fault in the appliance and the hot shorts to the appliance's case then the breaker in the genset will trip protecting you. So it all sounds ok to me.
Yamaha's instructions say you connect the ground terminal to your boat's engine
block/ground system as well as using the extension cord to connect it to the appliance. That way if a worn extension cord shorts to some piece of metal on the boat (other than the appliance) then the circuit breaker will trip protecting you from electricution if you were to touch that piece of metal. For permanently wired gensets, yes I agree. But for what you are doing no, the risk is very minimal.