Is Bayer really that bad? Their only problem that can't be denied is that they concede a lot of goals. Otherwise, they have kept the same will they had last season and one defeat doesn't change anything (or did you expect their unbeaten streak to be endless?).
Now the question is: are Bayern really that good? Yes, they scored 29 goals in 6 games, but who were their opponents? Ulm, Wolves, Freiburg, Holstein, Dynamo, Werder. Not a particularly impressive list, right? And Bayern conceded 2 goals from Dynamo at home. The game against Bayer will be their first serious game of the season.
From your analysis I see a very good point especially with the fact they Bayern has since this season not faves a really tough team or one that could be seen as their equals except for now that they will be facing Leverkusen in their domestic league but all others so far in their domestic league have been below their strength and their champions League performance was a show that they may not be really strong enough if they meet an equal opponent and their Leverkusen fixtures may be one of such to really show what they can be able to do against an equal. Let's just wait and see until Saturday what they will have to show.