You have to add Salzburg manually and select Germany as Country as Salzburg HBF is the offical railborder between Germany and Austria even as the political is few meters away. 

@Nanja Salzburg needs to be added to the destinations reachable with a pass valid in Germany. It has the same status as e.g. Basel Bad Bf, for which this has been implemented.

In General the borderstations should be have both Countries other examples are Passau (Austria/Germany), Kufstein(Austria/Germany) Bayerisch Eisenstein (Czech Republic / Germany), Simbach (Germany/Austria), Schaffhausen (Germany/Switzerland),St.Magareten (Switzerland/Austria), Buchs SG (Switzerland/Austria) For Rails Liechtenstein doesnt exist . Brenner (Austria/Italy) Tarvisio Boscoverde (Austria/Italy)

Tirano (Italy/Switzerland), Chiasso (Italy/Switzerland), Geneve (France/Switzerland) ,Basel SBB (France/Switzerland) Limone-Confine (Italy/France)

Außerfernbahn can be a bit difficult as “Transit” with a change in Pfronten/Reutte is a German tarif Route (Garmisch - Kempten) but if you stops along the route it´s Austrian tarif :D

This list are just the real Bordertarif Stations i know.

@seewulf Thanks so much! Juz had a look how to manually add the trip. May I confirm that all types of trains (e.g. EXP, RE, EC) are included in the Rail Pass as long as the location is from Munich to Salzburg?

The regionaltrains (RE), the Intercities (EC or IC) and the Railjets (EXP or RJ or RJX) should be covered. Iam not sure about Westbahn as the route is pretty new.
In general please dont use the Railplanner for planning the route please use a local app or website (Because of Liveupdates regarding delays / plattform changes) for Germany & Austria you can use either DB Navigator or Scotty (from ÖBB). Another app that´s quite good is Muj Vlak from Ceske Drahy (Czech Rail) this app combines a online mode and (if the packages are downloaded) even a quite actual offline mode.

The Interrail/Eurail Global Pass is accepted on Westbahn trains also in Germany, I’m not sure about the validity of Interrail/Eurail German Rail Pass.

Also not sure, if it is possible to add it via Railplanner App as train. 

unfortunately, this option does not work according to recent feedback :( This is one of the few instances where a one-country pass is used outside the country, and we are still working on the application for it.

As a workaround, please fill in the details of your journey until the last station before crossing the border and then travel the rest without having it added as part of your journeys in the app. Please use this page as a reference in case there's an issue with the ticket inspector (https://www.interrail.eu/en/interrail-passes/german-rail-pass the "Included destinations" part under the header Can I go to other countries with a German Rail Pass?). You can make seat reservations locally at the station.

Shouldn't be so difficult to solve, it seems to me. Chiasso works on a one country pass for Italy, even without having to add the journey manually.

The solution of @Annie. works very good on this route, where most of the Railjet Xpress (RJX) trains do not stop between Munich and Salzburg. So you enter without adding the train.

I have forwarded your feedback to the right department. This would be a great improvement!