It's not like this initiative disallows you from building other high speed rail connections. Just because a high-speed rail connection exists to Berlin doesn't stop you from making one to Munich.

On the contrary, the network effects of building out infrastructure means these connections would be even more useful. A high-speed rail connection from Rome to Berlin, for example, could hypothetically go through Milan, Lichtenstein, Munich, Nuremburg and Leipzig. This would mean all these cities on the route would benefit from connection to the rest of Europe.

EDIT: Also, looking at the map of Germany, connections like Budapest - Brussels also goes straight through Munich, so it'd probably be in that connection too