In reality it MAKES NO DIFFERENCE whether the motor is up or down when you tow it unless it's on a Sib.
The transom is built to take people giving it full throttle from stationary and being launched off waves etc.
Towing it with a car really isn't going to make a blind bit of difference and if the transom is cracking where the OP's is, it's from the top of the transom being pulled BACKWARDS-the way it is in normal use- or the cracks wouldn't have appeared there.
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