The voltage regulator inside the alt sets the charging system voltage. Nowadays the ECM is used as overhead to control that, it cuts back on charging at times when the alt is too hot and to save gas mileage and smooth up engine idle. If the vehicle is running fine with no problems accept it, all you will do is mess up expensive things.
The overall voltage setpoint is generally set in the main chip in regulator. That point is modified by the ECM as it sees fir, you will have to come up with quite a hack to override that. A 'tune' to change software could likely do it but $$$$$.
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