In Afghanistan, my team did PT separately. There was an expectation that everyone needed to be doing it 4 or 5 days a week, and the rest was up to the individual. Everyone, including our young, "not responsible" soldier, significantly improved their fitness because we were holding each other accountable and given the opportunity to challenge ourselves beyond what could be accomplished in a PT formation (my PT scores were always lowest in basic/AIT). Incidentally, that's basically how the whole FOB conducted PT, including a GPF company, and they all improved their fitness over the course of the year.
I think the key is to realize that if individual physical fitness is the goal, then PT formations are not the way to accomplish that goal. I don't see Olympic athletes or body builders standing in PT formations every morning. If the goal is something else, like someone's idea of what unit cohesion should look and smell like, well, I guess there's no arguing with that.
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