Ok,
Ive come to the conclusion, while considering a bidirectional DC/DC converter-solution, that a dedicated charge BUCK converter is the optimal approach for charging the secondary 3S2P battery. The MCU does not have PWM resolution to drive a BUCK converter at high frequency. It is possible to have the SAME51 do the switching, but the inductor value will have to be accordingly high and therefore large. Likewise the capacitors need considerable higher capacity.
Using the MAX17703 (60v to 12.6v) at a 1650khz freq. the inductor can be kept to 10uH. This charge IC has some clever safety features, like thermistor temp programming to suspend charge below/above eg. +5 to +45 Celsius. It has a pre-charge voltage setting, which will charge the battery at just 1/10 the MAX current until the CC (Constant Current) level is reached.
When the main (14 cell) pack is charging, the MAX17703 will draw current from the incoming charge current. Depending on temperature and other settings, the charge current can be set to low (60%) or high (50mV on shunt resistor).
Power_dissipation can be calculated using this TI BUCK_CALC sheet
