Total capacity do not depend on on the battery are plugged.
Setting them in series or in parallel will change how high voltage, or oh much current you can drain from them
They use two connector to balance the load through the connectors, and if you want to know how it work on the other side, why haven’t you looked at the CPi mainboard schematic? It is clearly shown there how the batteries are connected:
The diodes are there to procect the DevTerm, not the batteries. Obviously there is a charger and monitor system on the mainboard, the battery board is just to connect them, nothing else.
The proper schematic is here:
PS: the mainboard on the uConsole and the DevTerm are identical.