The only reason I could see re-flashing the PCM is if something was no longer stock in the trans (such as changing gearing ratios). Otherwise, the PCM should not care about it if it's equal to factory.
I'd be suspescious of what they are doing with a rebuild it a PCM flash is *required*.

 

hay i have a trans from them the only thing i had to do is swap out the wheel speed sensor it was not matching the speed i was going i was doing 70 when the speedo was saying 65. thats it to be honest .