I agree - it does not matter much. If the charge current is allowed to tail off to some small value then eventually I am sure the voltages will end up the same. If the charge is abruptly stopped whie in cc mode then the currents in the bus bars will tend to continue until the voltages across each cell balance and current goes to zero.Not to be to much of a stickler, but for doing balance charging, it DOES NOT matter much where you have your positive and negative leads. You are driving all the cells to the same voltage and the current will eventually drive to near zero. So no difference.
People get confused because when you install parallel batteries into a final configuration with an inverter and a charge controller, it DOES make a difference. The reason is that you are charging and discharging at somewhat high amps, and if you don't have the same path resistance to all batteries then some batteries will bear more stress than others. This is not applicable to balance charging. So, don't worry about iit.