I'm thinking Vogelhuber was filled in on what was expected of Johnson, and was told to do what he felt was necessary for his development. In my opinion, it was part of the reason he was sent down was to learn to be smarter with the puck. That situation was critical at that point of the game, a time he needed to be smart with the puck, which to me, makes his decision to sit him warranted. I still believe they called him back to quick, but they felt otherwise.
As far as Jenner goes, I don't know if they were playing him minutes to try to win, or to keep other guys at the minutes they were at for their development. I doubt they were really trying to win because I think they knew they weren't going anywhere anyway. I do think they had/have a plan in place to bring guys along at the pace they want to, and maybe throw them a few minutes more here and there if they were playing well enough, but Boone was simply eating minutes to keep the younger guys at the minutes they wanted them to get. Actually, Jenner's average time on ice this year was the least amount of his last 3 seasons, ( although it was only by a few seconds).