What you have seen is the complicated axle mechanism that rotated the cars. A motor did not turn the cars.
Underneath each car there is basically an axle that may, in your eyes, resemble a motor, but it is not a motor. This "axle" had a guide arm that rode on a rail that existed , basically, in between the tracks running rails. The rail that the guide arm rode on curved in and out depending upon the desired turn to the car. Every third car had an actual motor that propelled wheels that ran on the standard track. Just study the track of X at SFMM and you will get the same idea. There is a seperate rail that turns or rotates the seats throughout the course. It is the same principle here. No individual motors turned the cars, but they did power the entire length of cars along the track. Another way of explaining it is to think of locomotive wheels. The arm that extends between locomotive wheels is a similar principle.
For next year's Scooby attraction, the turn of the cars is being changed. And areas that you used to face towards will now be areas you pass with your back turned. To "change" the rotation of the cars at various points, the park has removed that inner running rail and is re-welding/bending/twisting/straightening it. That is why the PT cars are off in the first place. The work must be done with the cars removed. Once it is completed, the cars (every other) will be added back on and the guide arm placed along the new inner rail. When they fire the ride up, the cars will turn in new directions.
If we went by your thought that a motor turned each individual car, then it would not make sense that they removed the entire undercar mechanical unit. All they would have to do, in theory, is re-program the motors to turn at different times. For the change to "Mystery Machines" they could have just taken off the fiberglass shells and replaced them. That is not what they are doing.
Since you work at the park, I am sure you know one or two of the Technicians. Ask them sometime if they can tell you about it. Most of the time they can and will. I guarantee you that if they take the time they will explain the same thing I just did.
Go take a closer look at them... heck, take pictures if you insist. You'll only see what I have been explaining.
Shaggy