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The alternator wasn't intended to fully support the load demands of all of the electrical systems in the vehicle, it's there primarily to maintain the battery. It just happens that most systems can run off the output of the alternator, though.
The battery, in addition to providing high- current capacity for the starter, also performs much the same function as does a large-value capacitor in a high-power audio system. It smooths out the supply voltage and provides, on an as-needed basis, power when extra demand exceeds the alternator's capability to provide.
Keep in mind also that this truck has the newer PCM-controlled charging function. It's completely possible that there is a fault in that portion of the circuit and the alternator itself is not defective. This may also reflect in the ability of the parts stores to properly test an alternator on the bench. If they have an older machine, it may not support this generation of alternator.
Rezvani's Latest Post-Apocalytic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.