I've heard the same thing....that Ford engineers had a hand in on helping with the Whipple canned tunes which on the surface sounds real nice, but when you install a Whipple HO kit and you're basicly kissing the hp limit with your stock motor and the a/f ratio should be right on target for certain and the timing advanced to it's limit, then backed off a degree or 2 for some insurance. You just don't get that with any canned tune...period. I've read too many posts from guys with Whipple canned tunes that according to their dyno base runs showed the tune was way off. That's not to say that you couldn't get fairly lucky by chance, but the timing will be retarded to the point where the full potential of the system is way off like the 20-40 rwhp you mentioned in your post.

Kevin MacDonald of Diablosport who tunes my car said to never redline a blown 3 valve with a canned tune.

 

Makes sense. I guess paying the few hundred bucks for a dyno tune is better than 5k for a new engine.