Make the chipotle hot honey. Add the honey and 1–3 chipotle peppers to a food processor and blend until smooth. Use 1 pepper for mild, 2 for medium, or 3 for hot. Divide most of the hot honey into separate portions for basting and finishing, leaving 1 tablespoon in the food processor.
Make the marinade. Add the garlic, adobo sauce, lime juice, olive oil, smoked paprika, salt, and black pepper to the food processor. Blend until smooth.
Marinate the chicken. Pour the marinade over the chicken thighs and toss until evenly coated. Cover and refrigerate for 1–4 hours.
Thread the skewers and preheat the grill. Thread the marinated chicken onto metal skewers. Chicken thigh pieces will be flatter and more irregular than cubes, so fold thinner or longer pieces in half as needed when threading. Preheat the grill on high, clean and lightly oil the grates, then reduce the heat to low or medium-low, around 275–300°F.
Grill, flip, and glaze. Grill the skewers for 30–40 minutes total. Let the chicken cook undisturbed until it naturally loosens from the grates, usually around halfway through, then flip. Brush the cooked side with the hot honey reserved for basting and continue grilling until browned, lightly charred, and the thickest pieces reach at least 165°F. Remove from the grill and finish with the separate clean reserved hot honey before serving.