Your story illustrates that if they're bonded they're vulnerable. Spreading the charge increased the damage, and did nothing to protect the stern tube (was it bonded too?). If you isolate the shaft and engine block too, with relay disconnects such as Volvo Penta does, then you can place a zinc on your shaft and it will be sacrificial to a nearby boat with a charge. No?

I admit my understanding of this is a bit thin, so if I'm showing lack of knowledge please explain.