I´m interested to see the continuation of these series. I would have to bet on a few things as to why only the strength training population threw harder, though it is hard to say if they only benched or did tricep extensions.
Obviously I would not expect to see gains in the only practice group. Usually high level pitchers have efficient mechanics. If they didn't, they would not be there.
The medicine ball population seemed to do exercises that don't make a ton of sense to the pitching world. I would expect to see gains if they were doing drills such as the step behind shotput or something along those lines. Also, it is very evident that while you can only increase power so much, without strength, that power is useless.
The example of this is the two individuals who squat 200 lbs. One individual may have fewer fast twitch muscles which would cause less power production. However, if you increased his raw strength to, let's say, 400 lbs, if he produced 70% power as opposed to the 200 lb squatter with 100% power, he still would be producing more N of force (F=ma).
Therefore, there is a possibility that the strength training population increased the raw strength, and, with that increase, they were able to provide more force upon the baseball. Obviously a strength training program ought to not only increase raw strength, but it should also focus on increasing power as well.
Athletes who move better tend to better apply that force as well. You are only as strong as your weakest link, and for many that is movement impairment and lack of strength.
I look forward to Paul Nyman week.