If he can't hit target boost and he's only getting 16psi with the wastegate unplugged(should be getting over 20). It is obviously a mehanical problem with the turbo. could be bad actuator or cracked waste gate valve or boost leak. Since he said he said he went to a mehanic and got a leak test its probably some sort of wastegate problem.
computers don't magically fix mechanical problems. I honestly don't understand why people would mod a car at all if all your doing is paying a pro to do it for you. either buy an already modded car or jist buy a faster car. and the best advice people can give is take it to a pro?? Thats like saying "i have no real knowledge my advice is ask someone with real knowledge". Whats the point in even saying that?
it is possible that the tune could have caused some damage to the turbo, but the problem will not be solved with a new pro tune.