If the trolling motor has electronic controls it could be to protect the controls from overvoltage (voltage above manufacturers recommended)  or voltage spikes generated from connecting or disconnecting the charger leads w/charger power on .

For most 12V batteries standard charging voltages are 13.7V float ( 2.28V/cell) and 14.4V equalize (2.4V/cell). However, some cheaper chargers can produce voltages in excess of these. I would suspect the manufacturer is worried about protecting the trolling motor electronics.

Al Warner

http://www.zaltnad.com