Alright.
I came back to this question because of a German short story that just got published. In it the current leader of the German Catholic Church (GCC), Markus Domenikus von Rethagen, is called the chairman of the Conference of Bishops. That pointed to a much greater dominance of the GCC versus the Roman Catholic Church (RCC) than I imagined.
So, I asked about the influence of the GCC outside of the state of Westphalia (which the church completely controls). This was answered by sirdoom (see
http://shadowhelix.pegasus.de/Beitrag:Peer Bieber) who wrote most if not all of the recent stuff about the GCC for the German Shadowrun publications. According to him most German catholics are members of the GCC, but there are still some RCC believers left. Next to Westphalia the archdioceses of
Fulda (just a diocese today, possible that changed) and
Cologne belong to the GCC (though Cologne itself still has a significant number of RCC believers), whereas the
archdiocese of Munich-Freising is with the Roman Church.
Asked for clarification about the archdioceses of Hamburg, Berlin and Freiburg, sirdoom first points out that Shadowrun is not "Das Schwarze Auge" (which is of course the most successful German roleplaying system and sells a lot of setting books describing everything down to the colour of the prayer veils used in the seventh temple of the fifty-eighth small settlement to the right). Which is to say they have not divided all dioceses between GCC and RCC. So instead he offers a rough guide: the further away regional church structures are from Westphalia the more likely they will be RCC holdouts with the majority overall belonging to the GCC. He allows that probably none of the two churches holds much sway over Berlin.