For anyone wanting to try the "have the employee do it" I wouldnt bother. I've been told by more than 10 different employees over 5 or so different stores that "Yea, we can't adjust trade value" so it sounds like the ones doing it are acting on their own. A.K.A. a very rare Gamestop occurence.
FWIW, it was the store manager that did it for me earlier today. Only other person was in training, her first day I think. I just noticed the trade values were off for the two games, mentioned it to her and he came over, confirmed on the printed ad that all PS4 games have an added $5 and said he would just add the bonus himself. He took out a calculator and got the correct value that was missing from the bonus.
Edit: To the above question on the PS4 Pro, it automatically added it on.