Assuming the wire gauges are correct, wouldn't the size be based on the amperage draw of the system ? I think you could have a 200 amp alternator but doesn't mean it will produce 200 amp unless the system needs to draw 200 amp ?
Then wire sizing is based on the current draw of the equipment, and the distance and temperature of the wire route.
The circuit protection is then based on the wire size, unless you want to protect the equipment with a fuse.