I believe that to be the case. I'm currently going through some older batteries and trying to nurse them to life. Now I'm only working on one battery at a time, but from what I can see from the battery diagnostic software, once a cell reaches 3.6V the batteries internal BMS starts balancing between each of the other cells.
The battery I'm working on now shows a SOC at 93% and balance inactive. I gave it a little extra juice and one cell pack went up to 3.6V causing it to go into a balance active state. I presume the external BMS that is on the bike does much the same thing. When the bike is plugged in to charge it'll bring the SOC up to 100%, after that it'll start the battery to battery balancing. Which should also enable the internal balancing. While balancing the current flow would be minimal so that why the manual say to leave the charger on over night. I would imagine even longer in some cases.
Now I could be completely wrong with all this since I have little electrical background and I'm calling it as I see it unfold in front of me.