I think the thing about the upperclassmen not getting hurt- you have to remember that those pitcher are also older and more developed as baseball players and physically than the underclassmen who have not filled out yet and are still learning how to pitch. So, in general an older player can be more aggressive with weights and things like that.
And you are correct that pitching program shouldn't be one sized fits all because everyone is built differently and also at different stages of development physically.