You guys are missing that for this match they were playing Spain who are amazing in the midfield, so for defensive reasons Flick packed the midfield in a 4-3-3 with 3 players capable of playing as 6 or as 8, Goretzka Kimmich and Gundogan. Muller can't do that. It was either play him upfront, shove him to a wing, or take him off, no space for a #10 or a second striker on this shape.