The later model Ctek chargers will charge and maintain either type of battery as they recognize the type when hooked up. Both battery types take a different charge max and rate. In the 5.0l cars the charging system is different so I suspect they alter the charge to accommodate either flood or AGM. I don't believe the alternator is any different so maybe there is a programming change depending on which battery is used. The 4.2l cars use the standard charging method.