Yes there are some exceptions, but you're just proving my point: Even the Bahn can't negotiate full alignment across Germany although its only the largest of cities that don't accept the BC100 completely.
Then again, almost all of those cities have an extensive S-Bahn system, so we're really just talking about some subways across Germany where you still have to pay extra.
Case in point is Berlin: What edge case does it have to be for a typical BC100 owner to travel across Germany and have to visit Zone B or C with a subway but not with a S-Bahn?
It’s not an edge case. Zone B begins at the inner S-Bahn-Ring. There’s a lot of destinations that are reachable via U-Bahn and Bus/Tram outside the inner ring. It’s so common to travel outside zone A that you can’t even buy a zone A ticket, it’s always A+B
Keep in mind that “city” is only available for 120 cities in germany in the first place.
Then again, almost all of those cities have an extensive S-Bahn system, so we're really just talking about some subways across Germany where you still have to pay extra.
Case in point is Berlin: What edge case does it have to be for a typical BC100 owner to travel across Germany and have to visit Zone B or C with a subway but not with a S-Bahn?
https://www.bahn.de/wmedia/view/mdb/media/intern/cityticket_...