The basic idea of the counterbalance is to quell the vibration inherent with the engine design. The vibration induced in setting the pistons 90 degrees apart is different than the vibrati0on induced when the firing order is 360 degrees like in the old (pre 80's) Bonnevile motors (where both pistons hit TDC simultaneously). That's why the sound of the two bikes is different, different crankshaft firing order.
This is the Bobber crankshaft: Note the crank webs are 270 dgrees (90 degrees) apart. The delay in firing gives a more Harley like exhaust cadence.
The balancer shafts are actually counter-banacers to oppose the rotating mass of the crank pistons and webs. The amount of counterbalance can be tuned to totally eliminate the vibration (removing all motor character as well) or you can adjust the balancer to allow a certain desirable amount of vibration so it feels more "old school." That's why the balancer doesn't get rid of all the vibration it could. The factory 'tunes' the vibration into the machine. When the Bonneville was initially tested back in 2000 the engineers had 100% of the vibration quelled and when they compared the bike's 'feel' to a 1968 Bonneville it didn't feel right. That 1968 vibration was 'tuned' back into it. The 1968 Bonny wasn;t counterbalanced, it used a standard 360 degree crank firing order, where the mass of the pistons was counterbalanced by the crank webs.