You sound like an APR salesman. The APR+ is a weaker tune (than the standard APR Stage 1) that costs extra just so you can have a warranty for something that most likely won't happen. One of the major benefits of a custom tune is that it's tailored exactly to your car, your environment/weather, driving style, etc so it's running as strong and smoothly as possible. Plus with the Cobb AP you can monitor and log live data such as knock, AFR, boost levels so you can have the tuner iron out anything that could be a potential issue in the future. Ironically, APR is the only tune I've heard of blowing turbos or engines - granted that could be because they seem to be the most common choice
Those part-out sales are often from people getting ready to sell a car because
1) Unmodified cars are easier to sell, especially when dealing w/ the general public
2) You can get more money back by selling the aftermarket parts separately from the car