I don't buy the story that it's the same stress in baseball and softball. Baseball has a big history of pitching injuries and has been studied to death, thus at the major league level they limit pitches. Lot's of boys have blown out their arms by pitching too much and ended their careers. Seems to me it is much much much more rare in softball. More often than not, a softball pitcher will hurt their arm throwing overhand, not underhand.
The Baseball throw/pitch IS different than the windmill in multiple ways. In regards to the shoulder, the supraspinatus tendon is impinged under the acromion process during the acceleration phase of throwing, thus increasing the chance of rotator cuff strain. As the arm/rotator cuff tires, the shoulder joint becomes more unstable, thus increasing glenohumeral joint translation during phase 2 and 3 of throwing, thus increasing the chance of labral tearing. During the acceleration phase the shoulder is maximally externally rotated and abducted thus putting tremendous strain on the anterior glenohumeral ligaments, thus increasing the chance of capsular instability.
In regards to the elbow, particularly during the acceleration phase, the forces are concentrated primarily on humeral torque putting tremendous strain on the medial ulnohumeral ligaments with the elbow bent at 90 degrees. These ligaments will attenuate and even rupture at times, either requiring reconstruction surgery (Tommy John) or ending the athletes pitching career.
While the forces are also high on the arm of a windmill pitcher, they do not occur either at the same time in the throwing cycle, and the elbow position at the time of acceleration is extended, rather than flexed, thus causing less force across the ligament during acceleration. During the acceleration phase of the windmill, the supraspinatus tendon is actually being directed away from the acromion, thus reducing impingement on the rotator cuff.
What does this physiology mean? With proper mechanics the arm is
relatively spared from the forces seen in overhand throwing. When injuries occurs, it may be due to OVERALL body and mental fatigue, thus leading to a breakdown in mechanics, and eventual injury. In a perfect world an athlete and parent should have enough common sense to recognize this fatigue. When an athlete is blinded by by an overzealous coach, semi- irrational parent, or even from their own desire to overtrain-overpitch, the body can become vulnerable to injury. My DD is a pitcher who has had injuries, and I have been able to trace it's origins down to one of the 3 reasons mentioned in the previous sentence--believe me- it is humbling.