Doug Thorburn had a great read on Oswalt and Lincecum earlier in the year when Lincecum was struggling. He says that pitchers with small body types have to generate more power to throw hard. Because of this, they need to be in better physical condition to be able to repeat their mechanics pitch after pitch, game after game. Otherwise, their mechanics will slip and leave them vulnerable to injury. (DT is also the one that I have cited talking about Strasburg and the "injury cascade" from the shoulder to the elbow, basically blaming his injury on altered mechanics compensating for his shoulder... so he definitely values mechanical repetition).
http://www.baseballdailydigest.com/2010/08/22/raising-aces-os-mosis/
BTW, the Bauer article reminds me of another Verducci article on Lincecum (http://sportsillustrated.cnn.com/2008/writers/tom_verducci/07/01/lincecum0707/). I'd love to take a "chance" on Bauer. 
RIght, this is a major issue. Smaller guys are forced to use more of their bodies to generate velocity, while bigger guys can get by with the leverage advantage their bodies. As a result, they usually have "sloppier" and less efficient mechanics that rely more heavily on certain parts of the body, such as the shoulder. Through the years I have noticed that body type is not a very good predictor of injury, in fact there really is not a good predictor at all. There are certain motions that are more likely to result in injury. Also, as you mentioned, repetition seems to play a big role as. Another thing that scares me is when pitchers have hitches in their deliveries, as this creates timing issues and seems to nearly always result in some type o medical problem.
