Well, yes and no. You are correct that the balance board and the charger are differentiating between cell #1, and cell #2, etc. However, all of the cell #1's are connected in parallel, so the charger is seeing one conglomerate cell #1 and the "average" of all cells #1. So if cell #1 of battery A isn't keeping up with his buddy cell #1 of battery B, then the charge will end with that cell under charged (or the other one overcharged); or one cell may be dead altogether, and the charger wouldn't know it. No biggie once in a while, and if each battery is monitored. And it sounds like that is what you are doing when you said you balance them individually back at the shop and you are looking at each battery's health.
Just FYI, I am not speaking out of personal experience. This is purely what I have read and/or discussed with other operators that know more than me. Even though some of the people I've talked to do not like to do it at all, I still contend that once in a while, and if they are individually being cared for, then it is a very handy quick charging solution.