Bayern are unstable this season and they lost to outsiders both home and away, so with Arsenal the result could be anything in the return game, playing at the home stadium will not give Bayern significant bonuses. Let's say it will be difficult for Arsenal to win (this is 100%) but they can dry out the game (like in the game with City) and then there is a high probability that we will see extra time and a penalty shootout.
Bayern Munich will use all its strength in the Champions League match because there is nothing else that Bayern Munich can aim for except getting the Champions League title. But Bayern Munich's performance is quite dubious when compared to Real Madrid and Manchester City, which are more confident in getting the Champions League title even though they are wrong one of these clubs will be eliminated in this round but we don't know for sure who will be eliminated because they both look like they want to advance to the semifinals and look equally strong so if Bayern Munich faces one of these club I'm not sure Bayern Munich can beat it and It could be that Bayern Munich is eliminated by one of these strong clubs.
But what is clear is that Arsenal will still try as hard as possible in the second leg even though the chances are not that great because they have to play away. They can also do what Bayern Munich did, namely try to achieve a draw so that they can compete in the penalty shootout as you said, and by In the penalty shootout, Arsenal still has a chance to advance to the semifinals and Bayern Munich also still has a chance depending on which defense is stronger in blocking penalty kicks from the opposing club.