If you stay in your car, are you safest sitting with your seat belt on, or lying on the floor, or hiding in the trunk? This question assumes the tornado itself is coming your way and will arrive in one minute.
No, run to somewhere safe. Cars have windows, so the when the tornado comes, it can just pick you up with it. Hide in a basement or in a nearby bathroom where there is no windows. A place with closed walls. :D
This question begs another. What are you doing in the water ? In 18 inches of fast moving water your car - and you - are going places. If you are in a wash, you can figure the water is going downhill towards possibly a river Also, 18 inches of fast moving water can sweep you off your feet. You are in deep do-do. Tighten your safety belt, if you have anything like a blanket or anything soft - cover your head, duck low and wait it out.
The car will provide some protection from flying debris and the water should help prevent it from being lifted up into the air. If there is not a safer place you could run to and the tornado is already that close that flying debris is already an immediate threat, then a person in that situation probably should stay in the car. I would expect the windshield to be smashed, so if possible the person should cover their face and duck low, or lay down on the seat. Seat belts might help if the car is lifted into the air, but I would think flying debris would be the greater risk and that being lifted into the air is not as likely, plus if that happens, the chances of survival would be so slim even with a seat belt that I would just invest everything into avoiding the flying debris by getting on the floor if possible. There is more protection in the passenger areas than there is in the trunk, as the trunk is designed to collapse in to absorb energy from an impact, so if a person was in the trunk when the car was lifted then dropped on the trunk, then they would be crushed, while a person in the passenger area could survive the same type of impact. Depending on the car, there might be airbags, which are potentially dangerous.