For variety's sake, instead of backtracking to Vienna for my flight home after Salzburg I opted to keep going and fly out of Munich. It was a simple ticket purchase and a simple trip, just note the following.
I was staying at the Munich airport Hilton so I didn't need to go into Munich but was planning to change over to the S Bahn there. The ticket seller in Salzburg gave me a printed handout with timings and schedules for my trip but didn't explain that you can save a few minutes (and perhaps have a more pleasant station experience) by switching trains in Munich Ost instead of going to Munich Hbf. I didn't figure this out until I had looked at the printout for a while. So keep that in mind.
Also if you have plans in Munich or a tight connection, be aware that we had a security stop at the German border. Police officers boarded the train and walked through the cars looking for ... well I don't know because they just kept walking. Immigrants or stowaways I suppose, they did not ask everyone for their papers. We were stopped for about 20 minutes.
The train ride goes through pleasant scenery and then the airport is pretty far outside the city so it's nice. Munich station sadly was loud and gritty and seemingly had no eating or shopping options. It turns out there is an entire level downstairs full of such places but no signs indicating same. That's also how you will connect to the U Bahn and S Bahn trains.