A normal motorcycle battery does not have the amps a car battery does... now if you cut the ground with a master shut off switch, you still have power on the positive side of the ignition lurking for a ground. Any minor ground found wheather it be from moisture on an open terminal or what ever (static electricity also)... the power is there and will backfeed through the engine, it's mounts, the alternator or ignition system. Many of the components within the CDI electrically act as a one-way valve. If power is backfed through these components, with the amplified battery amps pushing it through the minor ground it finds the ignition box or even alternator regulator will be harmed.... positive cable power disconnect is the way to go..... eliminates any issue which could be caused by feeding the system in case it finds a minute ground anywhere
~Gimpster~