Preheat the oven to 400°F (200°C). Lightly grease an 8x8 or 9x13 baking dish depending on whether you are using the rice mixture.
Make 5–6 slits in each chicken breast to form pockets about 3/4 of the way through, spaced about 1 inch apart; do not cut all the way through.
In a small bowl whisk together olive oil, lime juice, lime zest, honey, chili powder, 1½ tsp salt, cumin, smoked paprika, onion powder, garlic powder, chipotle powder (if using), and ½ tsp pepper to make the Chicken Lime Rub.
Place the chicken in a shallow dish, pour the rub over it, and turn to coat evenly. Let rest at room temperature 30–60 minutes or refrigerate up to 8 hours, bringing to room temperature before baking.
Slice the bell peppers and red onion into very thin strips (about 1/8 inch thick). Stuff each chicken slit with one slice of red onion and one strip each of red, green, and yellow pepper.
Optional rice and beans layer: In a lightly greased 9x13 dish combine cooked rice, salsa, drained black beans, drained corn, drained fire-roasted tomatoes (if using), chopped green chiles, and the extra 1/4 tsp salt and 1/4 tsp pepper; spread into an even layer.
Arrange the stuffed chicken breasts on top of the rice-and-beans mixture or place them in a lightly greased baking dish if not using rice.
Bake uncovered at 400°F for 30–35 minutes, until the chicken is mostly cooked through.
Sprinkle Monterey Jack cheese over the chicken and continue to bake 5–10 minutes more, until cheese melts and an instant-read thermometer inserted into the thickest part reads 160°F. If needed, bake an additional 15–20 minutes depending on thickness.
Remove from oven and serve with optional cilantro, sour cream, guacamole, and an extra squeeze of lime if desired.