With the AMP gauge bypassed(red and black wires connected together) you are feeding the interior from two places. The MAD article has you connecting the red and black wires to the same fusible link in the engine compartment. If there is a short anywhere on the interior, that fusible link will blow. All power to the interior will be lost.
If you keep the black wire connected to the alternator, the red side of the amp gauge splice is the only side that's protected by a fusible link. If there is a short on the black side of the amp gauge splice, the alt will just keep pumping out amps and burn wires won't it?(possibly causing a fire) I would think that you'd also want a fusible link on the original black wire coming off of the alternator.
The MAD article ALSO shows a fusible link on the bypass wire from the alt to the relay.