good chance
I have a nissan 2.5 and have transported it from the shop where I bought it in my trunk. Closed all the fuel valves and breather cap and ran the gas out of the carb. Nobody at the shop thought twice to tell me that I can't lay it on its side to transport. They did recommend I do not transport it on the mount of the boat due to potential damage to the boat. As for the yamaha, my guess is - good chance you can.