In 2007 I had a few minutes as I changed trains in Neumarkt-Kallheim, Austria, some distance from the German/Austrian border. With nothing else to do, I explored the Austrian Rail automat there and was surprised to find it sold Bayern-Tickets.
Prior to 2012, I knew that there were some German Rail (Bahn) automats in the Salzburg station, on the platforms, and they, of course, would sell Bayern-Tickets. When I was there, in Salzburg, in 2012, I checked out the Austrian Rail automats in the Salzburg station, and I was surprised to find that they, too, sold Bayern-Tickets.
So, I think you will not have a problem waiting until you are in Salzburg to buy the Bayern-Ticket. If you do decide to buy it in advance, you should know that those tickets are non-exchangeable and come with the validity date printed on them, so make sure that's the date you want.
Regional trains from Salzburg to Munich are indeed a little slower, but it usually amounts to about a half hour difference. Once you get to Munich, a Bayern-Ticket can be used for any local transport in the MVV that day, so if your hotel is not right at the Hauptbahnhof or Ostbahnhof, you can use the Bayern-Ticket for the U-Bahn, streetcars, or buses to get to your hotel.