Just back from MUC and a lovely tour with the OberSalzburg too - I arrived on a Sunday and was off quick via a jetway but my CE bags took maybe 15 mins or more -
I had a car booked to take me to my hotel in the CC (Platzil) which was fast and no traffic - and no speed limits lol

As you only have really an hour to make the train I suggest a taxi to the Hauptbahnhof - or book a car to meet you like I did (mine was prepaid £50/56e) with city airport taxis dot com