One point that should be considered for all of these discussions is that the battery is NOT really the source for powering anything except the starter motor (or when the engine isn't running). The
Alternator is the actual source, but it has a three phase floating output (no grounds). Ground reference is not introduced in the circuit until the Rectifier, where the negative side of the bridge rectifier is grounded. So technically, for high power applications where you are unconcerned with any rectifier noise (ripple) you'd want to get your ground nearest to the source, and that would be at the Regulator Rectifier (RR).
But, you don't really want that for low power consuming sensitive electronic accessories. The battery acts like a giant shunt capacitor (low pass filter) and that is why you'd want to take your accessories' operating voltage from across the battery terminals; i.e. because that will be the voltage point with the least
noise.
In terms of fusing the wire run between the RR and the battery, the RR is still the main source and the battery is actually load (when recharging) and then a filter. Although things may be wired to the battery it is not the source except when the output from the alternator is lower than the charge on the battery. Putting a fuse closest to the R/R in that series circuit would protect the alternator and RR from burning up in the event of a short circuit anywhere downstream of it. But the battery would still smoke the wire. If the stock harness has no fuse or circuit breaker in that run between RR and Battery, I'd probably just physically protect the wires well (preventing shorts) and do the same.
The weak point (higher resistance) in this whole thing is unlikely to be the wire itself unless it is degrading over time. Did anyone try replacing the stock wire with a "jumper" of the same gauge?
The offending resistance is more likely to be in all of the connectors. You have connectors from the 3 phase generator, in and out of the R/R, and at the battery end, as well as any connections in ground path continuity from R/R to battery. Adding in a fuse or circuit breaker adds two more connections that can add resistance.
The Honda VFR800 charging systems had lots of issues in this charging circuit too. Some of the effective "fixes" involved eliminating as many connectors as possible. These quick disconnect points are really not important except for when you need to replace one of the components. For the number of times we need to replace an alternator stator or R/R we could just do straight hi-pressure butt splices, and even solder fill the splice if desired, and get rid of several weak connection points. The only downside is that when you did have a component failure you'd have to cut them out and re-splice.
