Melt butter in a small saucepan over medium heat.

Remove from heat and stir in honey, orange peel, lime zest, thyme, chipotle chilies, cumin, and salt to make the citrus glaze.

Freeze the glaze until it firms up but is still spreadable, about 30 minutes.

Set aside 1/2 cup of citrus glaze for the gravy.

Melt butter in a large nonstick skillet over medium-high heat.

Add onions and reserved turkey parts (neck, gizzard, heart) and sauté until the onions are very deep brown, about 22 minutes.

Add carrots, celery, and tomatoes to the skillet and toss to blend.

Preheat oven to 400F and set rack in bottom third.

Place a small rack in the center of a large roasting pan.

Sprinkle the vegetable mixture with turkey parts around the rack.

Rinse turkey inside and out; pat dry.

Place turkey on rack in roasting pan.

Starting at the neck end, carefully slide your hand between the skin and breast meat to loosen the skin.

Rub 1/2 cup of citrus glaze over the breast meat under the skin.

If stuffing turkey, spoon stuffing loosely into the neck and main cavities.

Tuck wing tips under turkey; tie legs together loosely to hold shape.

Brush 1/3 cup of glaze over top and sides of the turkey (not the bottom); reserve any remaining glaze.

Sprinkle turkey generously with salt and pepper.

Cover turkey loosely with foil.

Roast for 30 minutes.

Reduce oven temperature to 350F; add 1 cup of broth to the pan.

Press foil snugly around the turkey (not the pan).

Roast for 1 hour 15 minutes.

Add 1 cup of broth to the pan.

Roast turkey until a thermometer inserted into the thickest part of the thigh registers 175F, adding 1 cup of broth every 30 minutes, lifting foil to baste with pan juices, and removing foil during the last 15 minutes to brown the turkey, about 3 hours 30 minutes longer if unstuffed or 4 hours 15 minutes if stuffed.

Transfer turkey to a platter.

Tent with foil; let stand for 30 minutes (the internal temperature of the turkey will increase by 5 to 10 degrees).

Reserve pan juices.

Strain pan juices into an 8-cup measuring cup, pressing on solids to extract pulp and liquid; discard solids.

Spoon fat from the top of juices; discard fat.

Add enough chicken broth to the pan juices in cup to measure 6 cups.

Stir reserved 1/2 cup of citrus glaze in a heavy large saucepan over medium heat until melted.

Gradually add flour; whisk for 1 minute.

Gradually whisk in pan juices.

Bring to boil, whisking until smooth.

Reduce heat to medium; boil until sauce thickens slightly, about 5 minutes.

Season gravy with salt and pepper.

Brush any remaining glaze over turkey.

Serve turkey with gravy.