The reasoning behind the stock system is the EQ curve of the DSP (digital signal processor) changes with volume settings. Bass is reduced and treble increased as you turn it up. For this reason, when you run an aftermarket amp, you must flash the head unit to flatten the EQ curve via Digital Technician ( computer at HD) to the specifications of the atermarket amp you install. With the correct flash, the EQ curve is flat across the volume range allowing the amp to do what it's supposed to wherever the volume is set.
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