In a large baking dish or roasting pan, mix molasses, vinegar, bourbon, pepper, garlic, shallot, ginger, thyme, and chili flakes. Trim any excess fat from tenderloin and discard. Rinse meat and pat dry. Set in marinade and turn to coat. Cover dish and chill, turning meat occasionally, at least 4 hours or up to 1 day.
Lift beef from marinade; discard marinade (or bring to a boil, cool, cover, and freeze for another use). If tenderloin is uneven, tie with cotton string where needed to make evenly thick. Set on a rack in a foil-lined 12- by 15-inch roasting or baking pan.
Bake in 400° regular or convection oven until a thermometer inserted in center of thickest part registers 130° to 135° for rare, 40 to 50 minutes. Let rest in a warm place at least 5, or up to 15, minutes.
Remove strings. Transfer meat to a platter and garnish with parsley sprigs. To serve, slice 1/4 to 1 inch thick. Add salt and more pepper to taste.