It was not completely unusual among some European families that used two or three names or a compound name to use the same "filler" name as familiar tradition.
In English the first name is usually the main name, but this use is not universal.
In French, the concept of "middle name" is inexistant as in many languages (Spanish, e.g.). In case of several names, it can be a compound name or a set of names, where the main name is usually the first, but not necessarily: Aurore Dupin, aka George Sand (in fact, Amandine Aurore Lucile Dupin).
In German the use of the second name as main name was usual: Wolfgang Amadeus Mozart (in fact, Johannes Chrysostomus Wolfgang Theophilus Mozart), Johann Christoph Friedrich Schiller, Eugen Berthold Friedrich Brecht, Wilhelm Richard Wagner...
So Bach brothers probably were known by their second name (Rudolph, Sebastian, Christoph...).