I think the absence of Harry Kane wouldn't really affect their performance in Bundesliga, I believe they can still able to win against Dortmund. As long as Muller and Musiala are playing, they don't have to worry against mediocre teams.
But when it comes to Arsenal in Champions League, I'm not convinced Bayern Munich will win. It's The Gunners games because the match will held in Emirates Stadium.
I think these two teams are not easy for Munich to face, Borussia Dortmund is not a mediocre team, it is a top team in the Bundesliga, the same as Munich, so the absence of Harry Kane will definitely really affect Munich in the upcoming match, and what is certain is that Munich's attack without Harry Kane will be a bit decreased because Harry Kane is a goal scoring machine for Munich so I'm not sure Munich will be able to win the match against Borussia Dortmund later.
So, that is Munich's problem at the moment, even though Munich wants to fight harder in the UCL to get a trophy, but if one of the important players is absent, it will definitely be very difficult for them.
You are right, BOrussia Dortmund is not the mediocre team mentioned, they are one of the top clubs which is experiencing a decline this season, so they have to be in a position they are not used to, because usually they are always in 2nd place in the standings. This is a match that will not be easy for Bayern Munich, because they have to face a club that is their rival. What makes them at an advantage is that the club they will face this time is not as strong as the previous season, but still they cannot just underestimate Borussia Dortmund.
Apart from this match, they also have a match that is no less important in the Champions League, because the result of that match will really determine their position, whether they will still be in the Champions League, or whether they will have to pack up and be eliminated from the Champions League. Looking at their opportunities in 2 different competitions, it looks like Bayern Munich will focus more on the Champions League, because in the Bundesliga their chances of becoming champions are almost closed.