You make something very simple seem complicated. It really isn't.
Well, having given everyone the chance to contest that statement, I'll tell you why it is actually a bit more complex.
In an FX-3 or EX-3 the ignition modules are powered directly from the battery and are powered regardless of the state of the Master contactor. They only draw a few micro amps when the ignition switch is Off.
When the alternator is working and charging the battery, the shunt current (AMPS display) is the sum of the battery charging current and the current drawn by the two ignition modules. Any system load (lights, strobes, avionics, etc) is powered directly from the alternator and this current does not pass through the shunt.
When the alternator fails, if MASTER remains On, the shunt current (AMPS display) is the system load (lights, strobes, avionics, etc) but does not include the ignition module current. The actual battery discharge current is now AMPS readout plus about 2.4 A for the ignition modules.
This does not change my position that zero amps is the correct threshold for AMPS alerting. However, it may provide some insight on how to interpret the AMPS reading, particularly when load shedding after alternator failure.