The blog says that failing to land on the carrier didn't actually fail the mission. Maybe you're misremembering? I just remember this game being so frustrating that I never replayed it.
I also clearly recall it failing the mission, could there possibly have been different versions of the game? I've heard before of Nintendo distributing slight variations of the same game based on region back in those days, perhaps that's what's going on?
You did lose a life; so if you failed the landing, then the in-air refuel, then the landing it was game-over at the end of the second level.