Well hell, all I can tell you is the reports on his velocity were in one band for the first few years of his career and then this year the reports were that he was throwing harder.
I don't have access to reliable minor league data on pitch velocities beyond what is reported on twitter, so I would agree that you shouldn't present my observations in a scientific paper or call me as an expert on the matter at trial.
My best guess though is he was throwing a little bit harder this year.
...
I have no idea what his throwing regiment was before or after he got to Atlanta so I'll totally bow out on that one. Could be.
I think shoulder injuries are probably pretty random though rather than some systematic defect in a team's approach. Also just a guess.