Hi Scott.
It does not matter that the two BMS 'sees' the same volts at the positive end of the connected batteries. Each BMS works independently and looks after the 3 cells in its 'battery'.
The amount of current flow during charging is determined by the 'internal voltage generator' in each set of cells. This generator increases with the state of charge. Should the SOC differ then the battery with the lower internal volts will get a bigger share. The net result is that the batteries self balance.
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Mike