the junction is really just a way to group wires... Right?
yup, correct.
AFAIK the 'brain' of the system is the junction 'A' box which can also tell you your battery level , and let you fine tune the rear derailleur position (if you hold down the small button,then click the shift levers to adjust.)
The shifters are the control point. They send the signal (the shift) to the motors on the deraillers,which do all the work.