I am guessing that their situation at Bundesliga would not hurt them in the champions league, looking at the current situation you could easily see that they are not really staying behind. That decisive win against Barcelona showed that even though we have seen Bayern Munich ending up with a bad results in bundesliga, they are still playing very well in UCL.
We need to realize that they have been playing very well in UCL for a few years now, first the championship and before that and after that they have been pretty nice. Which is why I am guessing that they are going to keep being good, finish at the top of the group and going to be at least in quarter finals.
Bayern performance in the UCL is not in doubt because they can always qualify for the semifinals and with their inconsistent situation in the Bundesliga I think it's not a big problem for them because Bayern have a busy schedule so far so they prioritize the UCL over the Bundelsiga because in bundesliga they will find it easier to improve the rankings when they are not on a busy schedule. well from this situation I tend to be more worried about the fate of chelsea where they are very inconsistent in the domestic league or in the ucl. I hope Chelsea can improve their performance.