I am skeptical here, and I appreciate your use of the word supposedly, mainly because the whole conditioning thing appeared to me to be a knee jerk reaction to the result of the 2011 season. I think there is a fair amount of red herring in that argument. Maybe it will be markedly better in 2012 due to changes in the staffing. However in the MLB the strength and conditioning guys are glorified towel holders when you compare them to their counterparts in the NFL just as an example. The amount of actual control that an MLB team can exert on a player is a paper tiger compared again to the NFL equivalent. The player himself, more than any of the four major NA pro team sports is more responsible for his own conditioning.
One could even at least argue that the number of legitimate training regimens that have been developed strictly for baseball are a paltry few compared again to a sport like football. Ya' wanna' keep the muscles required to swing the bat effectively, supple and sound, hopefully avoiding injury? Pick up a bat and swing the hell out of the thing. Ya' wanna' strengthen your throwing arm? Pick up the ball and throw hell out of it.