What they did in the league after they have won it is completely and totally meaningless. Say they beat Hoffenheim, Augsburg and Dortmund. Then what? It would just make the statistics look better.
Last season, other big European teams, such as Juventus and Barcelona would not have faced Bayern with fear and dread. This is not the case this season. This is a massive and crucial difference, far beyond any potential effect that any manager/tactics could have. The fact that the rest of the elite clubs are willing to be largely negative against you, and not completely falling into your trap as Barcelona did, changes everything.
And one more thing, I think that the 4-0 aggregate scoreline over Juventus was somewhat flattering for Bayern, while the 7-0 over Barca was just a joke. Bayern definitely the better team of the two, but some of the goals in the first leg were dubious at best, while the 2nd game was a formality. Remember that even last season's Bayern had a very hard time against both Arsenal and Dortmund. No team is invincible in football. Simple as. You can be mixing your tactics all you want, when you play against Real Madrid at the Bernabeu, the chances of you losing, are quite high.