That makes sense. The Prodigy setup for the wastegate can cause over-boost in partial throttle transitions. Since that setup is trying to get the manifold pressure up to the target (~8.2 psi), there can be part-throttle conditions where the turbo produces more than 8.2 psi prior to the throttle body while trying to make the pressure after the partially closed (restricted) throttle body reach 8.2 psi. In this situation, opening the throttle more reduces the restriction and can cause a temporary surge in boost as that excess pressure behind the throttle body is now allowed to enter the intake manifold.

During full throttle acceleration, it won't make a difference because the pressure is the same on both sides of the throttle body at full throttle.