It means, shut the breaker off to the battery charger before you start the boat. The alternator is sending a charge to the battery when the engine is running. They don't want the alternator and the charger both attempting to charge the battery simultaneously. Also, I suspect the spike in voltage when the alternator is charging could confuse the battery charger.
Normally, I would disconnect the shore power before starting the engine. I typically shut all the breakers, including the mains, before I disconnect the shore cord. Then I start the engine.