Hi Kent:

I have never seen a diagram of the "bonding" system. (yellow/green wires to sacrificial anodes).

As to your other question, as to why the bonding system isn't tied to the battery -ve (negative) post.  I can postulate this theory.   

The bonding system is a protective system designed to carry any stray current/leak current and any galvanically induced current to the sacrificial electrodes.  Amel wanted the DC circuits to be isolated from protective system as those circuits have current flowing thru them any time a DC circuit is in use.  Those circuits should stand on their own, ideally isolated from the bonding circuit and not having leakage current as the electrical componentry normally is "insulated" from that part of the appliance that is in contact with seawater.  In this way the protective circuit only comes into play when there is leakage current from a DC device (due to a fault) or if there is a galvanically induced current from two dissimilar metals (thru hulls etc) and the anodes. .  Remember the case or fitting of any metal object in contact with sea water is tied to the bonding system.  The alternator isn't in contact with sea water.  Its electrical componentry should stand on it's own and in the Amel strategy  the electrical componentry should be isolated electrically from the engine.   If you tie the bonding system and the DC battery negative together you put the protective circuit "on line" with all DC circuits all the time.  Additionally you now provide a parallel pathway for EMF in the seawater (perhaps from a nearby boat with an electrical fault)  to push current via the bonding system, into the DC system where it seeks ground at the battery (electrically we say sinks to ground at -ve).  The DC negative should NOT be connected to the bonding system.  The DC circuits and the bonding circuits should be separate circuits.

Again, not sure I clarified or muddied the waters.  If muddied, let me know and I will try again.