Puree the sesame seeds with the cocoa powder, chipotles, adobo sauce, tomato puree, onion, cilantro, ½ teaspoon salt, ¼ teaspoon pepper, and ½ cup water in a blender until smooth.
Heat a large saucepan over medium-high heat and add the sauce. Cook, stirring often, until thickened, 10 minutes. Transfer 1 cup to a bowl and refrigerate for 15 minutes.
Heat a grill pan over medium heat. Season the zucchini wedges with ½ teaspoon salt and ¼ teaspoon pepper. Grill, turning, until charred and tender, 10 minutes.
Toss the chicken with the chilled sauce, 1 teaspoon salt, and ½ teaspoon pepper in a bowl. Grill, turning, until cooked through, 25 minutes.
Serve the chicken and zucchini with the rice, the remaining mole sauce, and the lime wedges.