Voltage regulator overcharging

When everything is off, voltage from ground to battery positive is battery voltage.
When the engine is running, voltage at the battery positive is alternator output voltage, minus any drops due to resistance in flow. In any event, its not battery voltage.

If the key is in the run position, and the blue wire is less than 14.2 V, the voltage regulator will allow current through the alternator's field.
Blue wire is the regulator voltage 'sensing'
Blue wire supplies power to the alternator's field.
Green wire is the alternator field's ground. The regulator contains the 'switch' that allows the ground circuit to complete unrestricted, not all all, or something in between depending on the voltage in the blue wire.

A couple diagrams here that may help..
main_charging_wires_plus-off-png.png