Preheat the oven to 500˚ and arrange the oven rack in the center. Remove the innards of the duck and reserve them for another use or discard. Remove any loose pockets of fat surrounding the cavity. Season the inside of the duck with salt.
In a pot large enough to hold the duck, combine 6 cups water, 3/4 cup of the soy sauce and 1/3 cup of honey. Bring the mixture to a simmer over low heat. Add in the brine from the green peppercorns, lower the heat and submerge the duck, breast-side down, in the pot. Let it simmer 30 seconds, basting the top with the liquid. Remove the duck and arrange it, breast-side down, in a roasting pan fitted with a rack that elevates it off the bottom of the pan. The rack will allow hot air to circulate around the duck as it cooks. Tie the legs together with kitchen twine.
Put the roasting pan in the oven and turn the temperature down to 400˚. Cook for 30 to 35 minutes, until the duck is well browned. Remove the pan from the oven, then flip the duck. Using a turkey baster, remove the excess fat from the bottom of the roasting pan and transfer it to a heatproof liquid measuring cup.
Return the duck to the oven and cook for another 45 minutes to 1 hour, depending on the size of your duck, or until well browned all over.
When the duck is almost done, in a medium pot, combine the vinegar with the remaining 1/4 cup soy sauce, 1/4 cup honey, the Marsala and the green peppercorns. Bring the ingredients to a boil over high heat. Lower the heat and simmer gently, allowing the glaze to reduce to a thin syrup and the flavors to blend, 10 to 15 minutes.
Remove the duck from the oven and baste it with the drippings in the bottom of the pan. The duck should register about 150˚ when an instant-read thermometer is inserted into the thigh meat. Transfer the duck to a platter and pour half of the glaze over the breast and thigh meat. Reserve the remaining glaze for plating. Allow the bird to rest for about 15 minutes. Carve the duck and arrange on a serving platter. Season the flesh with salt, if desired, and top with the remaining glaze. Reserve any fat that accumulated at the bottom of the pan and use for the onions.
For extra-crispy skin, let the duck sit overnight in the fridge after simmering.