The short answer is if you are just swapping out the alternator and you need it for a trip, don't worry about it. You don't need to upgrade wiring if you don't have things that use high amps.

After looking at the wiring diagram, it seems like Isuzu is using the fusible link box as a distribution block of sorts. It provides power to the lighting circuit AND protects the rest of the electrical.

So, to fix this you could do it in a few ways. You could run 4ga wire directly to the positive post of the battery and remove the between the alternator and the fusible links. You could also probably leave the wiring as is, and add another 4ga between the alternator and the battery. The fusible links are still getting power from the battery and one of the links is protecting the battery side of the circuit. You don't need circuit protection on the charging side of the circuit.

I think my prefered route would be to add the wire to the battery and leave everything else. That way the lighting circuit can share the load when the engine is running, instead of running 100% of the amperage through one side of the supply to the fusiable links.

But, when you add things (stereo, lights, winch ect) they will need individual protection related to their individual loads (this is where you could use the 200A fuse on the winch, for example), but they will need to be wired off the positive post of the battery (either directly or through an appropriate distribution block).

Clear as mud?

Good Luck,
Michael