Make the citrus marinade by whisking together orange juice, orange zest, lemon juice and zest, lime juice and zest, minced garlic, minced shallots, olive oil, brown sugar, salt, pepper, fresh rosemary, dried parsley, and red pepper flakes in a large bowl until the sugar dissolves and everything is well combined.

Pound chicken breasts to an even ¾-inch thickness or butterfly them in half horizontally. Pour half of the marinade into a shallow dish or resealable plastic bag, add the chicken, and turn to coat completely. Reserve the other half of the marinade in a covered bowl in the refrigerator for the glaze. Marinate the chicken for at least 30 minutes or up to 4 hours in the refrigerator. Do not marinate longer than 4 hours.

While the chicken marinates, prepare the citrus glaze. Add the reserved marinade (the half that never touched raw chicken) to a small saucepan with 2 tablespoons of honey. Bring to a low simmer over medium heat, stirring occasionally. Simmer gently for 5 to 6 minutes until it reduces and thickens enough to coat the back of a spoon. Remove from heat and set aside.

Preheat grill to medium-high heat, around 400°F. Clean the grates and brush with oil. Remove chicken from marinade, letting excess drip off. Discard the used marinade. Place chicken on the grill and cook for 6 to 7 minutes per side until an instant-read thermometer inserted into the thickest part reads 165°F. During the last 1 to 2 minutes of cooking, brush both sides generously with the prepared glaze.

Transfer grilled chicken to a clean plate and let rest for 5 minutes before slicing. Slice against the grain and serve with extra glaze drizzled on top or on the side.