The important thing to notice is that in this Bayern-ish system brought by Herr Flick, Lewandowski can finally find his "space" of play.
In Xavi's system, he was on a wild goose chase everywhere on the pitch and it was a sore to an eye to watch due to the fact that he's not capable or at best has mediocre skills to assume a midfielder role at this level of intensity, speed and precision, thus often looked like a tractor, indeed, who slowed things down and threw off the tempo of play.
Now, Flick, utilizes him in the classic definition of what the #9 is. I suspect, it had to be adequately lectured and conveyed to Raphina and Yamal, also Balde and Ansufatti, who have this natural thrust towards goal and finalization, that the days of false 9 are long gone and to orient their play around the real target man instead.