There is no good reason behind changing it. The job is to balance the engine with the flywheel spec'd for that motor. I've done a lot of these swaps and can verify it will not make any difference.
There is a slight difference in balancers based on the vehicle the motor was intended for. The GP guys frequently look for and put Bonneville balancers on their motors to smooth things out further. Some of the balancers are more refined for the luxury car super smooth running feeling. I'd think the PA and Bonneville would be the same balancer though.