They are using the old "better safe than sorry". I think the chances of damage are generally low. There would have to be some unusual circumstance to cause damage. Electronic modules in 12V based cars are usually built to withstand 16V continuously (24 hours) and "load dump" transients up to 80V briefly and they can usually withstand reverse voltage briefly. One problem could be hooking up a charger to a battery with loose connections, so that the battery does not load down the charger and the voltage floats up to some high voltage. So then the car is seeing the high voltage but the battery is not. I would say just hook up the charger and put a voltmeter on the clamps and make sure the voltage is below 16V. If it is then you should have no problem.

Mike

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1998 C230 330,000 miles (currently dead of second failed EIS, yours will fail too, turning you into the dealer's personal human cash machine)
1988 F150 144,000 miles (leaks all the colors of the rainbow)
Previous stars: 1981 Brava 210,000 miles, 1978 128 150,000 miles, 1977 B200 Van 175,000 miles, 1972 Vega (great, if rusty, car), 1972 Celica, 1986.5 Supra