Ya got me!
But I'll bet that if I remember to ask him next time I see him he will provide me a sketch with 27 circles and arrows and paragraph on the back describing what each one was about.
But here is my plain old guess.
The well pump was bonded with a grounding connector sized to the circuit that was providing power to it. The well pump was solid iron bolted directly to the well. So the 'electrode' was bonded to the pump with nuts and bolts.
With the bonding cable from the well back to the panel there would be three paths for a ground fault to take.
1) The bonding conductor that the inspector made go away.
2) The grounding conductor in the cable that feeds the pump.
3) Through the earth to the other grounding electrodes and their conductors. In this case, both the well and the city water supply were excellent electrodes due to their size and continuous contact with wet earth.
Three parallel conductors of different impedances certainly does make a case for ground loops, but so doesn't two?
I am sure as per the NEC he was right, I just don't know exactly why.....