I can speak about the Yanmar 6LY, but apparently the 6LP is the same. The coils are in the intake after cooler and sit on top of it. You can unhook the wires to them and see if it makes any difference in smoke. With them unhooked the voltages and alternator will act normally and the voltage should immediately rise to 13+.
They unscrew from the top of the after cooler and it sounds like they are the same as the 6LY so you can replace them with a blank plug you can buy from Yanmar. Or you can just clip the coil so it won't be in danger of corroding and breaking loose someday.
I believe that the coil is controlled by engine temperature. Mine takes about 5 minutes to turn off in warmish ambient temps.