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"I'm just wondering if the normal fuse between the starter and the terminal box would have prevented the fire. It seems to me like it wouldn't since even if it had a fuse and the fuse blew, that the generator would continue to output."
On the original stock generator, the battery is the only control for the output, so if you have an open in the charging circuit the generator has nothing to control the output and the generator keeps raising the voltage until it meets the limits of the design, which is about 40 volts. 40 volts will cook the generator.
If you have a SHORT, then the short becomes the reference for the generator output, and the generator will be safe at 0 volts because the output is directly shorted to ground. But since the short is also being fed by the battery, something will burn up, either the fuse or the wires.
The EVR (electronic voltage regulator) will help give the battery the correct charge under varying conditions, as needs dictate, and it will also limit the output voltage to a safe level if you should have an OPEN in the charging circuit.
It sounds like you had a short in the lights/horn circuit. Did you have the lights on when the trouble happened?