It appears that the direct Prague to Munich bus no longer goes to (leaves from) the Munich Hauptbahnhof. Instead it uses the ZOB (Zentrale Omnibus Bahnhof) at Hackerbrücke. Then you have to take any S-Bahn from Hackerbrücke to the Munich Hbf (approx 11 min including a 10 min walk). If you put in "Munich Hbf" on the Bahn query page, it will come back with a Saving Fare ticket only to/from Hackerbrücke. But if you spell out "Munich Hauptbahnhof" it will offer a Saving Fare ticket including the S-Bahn (non-train-specific) between Hackerbrücke and the Hbf.
Also, it appears that they no longer offer a Savings Fare ticket for the IC Bus between Prague and Nürnberg and the ICE to/from Munich Hauptbahnhof.