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The module that commands the charging system failing to command it correctly, so the alternator is not asked for what the battery needs. Modern alternators do not self-regulate to a fixed voltage — a module decides the target based on battery state, temperature and load, and communicates it.

So the alternator can be in perfect condition and still not charge properly. The complaint is under- or overcharging with an alternator that tests correctly in isolation, which is exactly the case a bench test cannot detect. Read the commanded charging voltage against the measured one: they should track, and a measured voltage that ignores the command is the alternator, while a command that is itself wrong is the module or its inputs.

The inputs are usually the problem rather than the module. A failed battery monitoring sensor, or a new battery never registered to the vehicle, leaves the module commanding a target appropriate to a battery that is not fitted. Check those before condemning the controller.