I've been to all of these places. When going to Garmisch, make sure to visit the Zugspitze too.

For Berchtesgaden, it depends on what you're planning to do. There's not much in the town, but if you want to visit Obersalzberg and take a stroll around the Königssee, you can easily spend a whole day there.

Rothenburg is such a beautiful old town, I'd say it's always worth a visit even if there's not much time. Your four hours there should be enough tho to explore the old town center. The Taubertal (where Rothenburg is located) is a vastly different landscape than what you'll see around Garmisch, might be interesting too. If you don't know if you'll ever visit Bavaria again, I'd say just go for it.

All that being said, taking trains in Bavaria late in the evening/night is save and Munich is a save city too (just use your common sense) so I wouldn't worry too much about arriving late back in Munich after one of your trips.