It's just one of the ways you can use Messi. Messi is surprisingly versatile, but even if he's played as an AM rather than a F9, he can still be shut down by the big teams, and that's where all of Barca's problems arise. When Messi is shut down, the Barca system collapses, and I think that putting him deeper enables him to start his runs from further out, so that stopping him is more difficult.
But remember one thing, and that is the wingers are nowhere near as good as Messi (which means less goals for Barca if all the chances fall to the wingers instead of Messi), and that good teams can just mark properly, and Messi won't get a wink of the ball (which means the wingers won't touch it either). If Bayern can shove players up to mark players who play as deep as Gerard Pique and Sergio Busquets, I don't see why they would have much difficulty positioning themselves to try to mark Messi. Either way, Messi's style is so freaking predictable that if you get a couple guys to position themselves properly, he doesn't get a touch of the ball (notice that he always picks up the ball, and continues to drift to his left, and eventually unleashes a low shot, gives a slick pass to a winger, or dribbles through the defense).
Here is the last 2 indivudual highlights of Messi, he couldnt find enough space to score but he gives other players a lot of freedom.
Its more and more complicated for Messi to get the ball at good conditions in big games and against wise coaches, who knows how deadly he is, and how barça is weak when Messi is marked constantly.
His presence in the attack makes our moves predictible, and makes it complicated for us to score.
Messi needs more and more to move back to the midle to get the ball having no freedom even there.
So, imagine now Messi doing like Rooney taking the control of the midlefield, giving accurate crosses to our good wingers (Neymar, Pedro, Alexis and Tello who all scored a hattrick recently and being in a good form).
That will completely change all the tactics elaborated against Messi, as if he is marked in the midle, wingers will be more free at the wings, and can get the ball by a long accurate cross from Messi,Iniesta or Cesc. it will also let other players play at full potential WITH Messi and not FOR Messi.
What do you think about this guys ?