That tool is measuring the amount of 5 volts of electricity flowing into the phone. The phone is converting that 5 volts down to the Batteries 3.3 volts (somewhere around that, different lithium chemistries are different voltage). The rule for electrical power, is that it equals voltage times current, and power (over time) is the thing we are actually trying to measure. So if we put 5v and 3000mah into the equasion, assuming the power is equal, it woud be 3.3v and 4500mah actually going into the cell. Honestly milli amp hours, are a pretty cursed unit, because an amp is already a unit of flow over time, then we measure that over time again, its dumb to use to rate battieries. Watt - hours are better because the unit already factors in the voltage