Place yellow onion, habanero peppers, green onions, lime juice, soy sauce, garlic, fresh thyme, brown sugar, oil, salt, black pepper, allspice, dried thyme, cinnamon, cumin, and nutmeg into a blender. Blend until marinade is completely smooth.
Place chicken drumettes into a large bowl. Pour marinade over chicken and toss to coat completely. Cover the bowl with plastic wrap and marinate in the refrigerator for at least 8 hours to overnight.
Preheat the oven to 450 degrees F (230 degrees C). Line a baking sheet with aluminum foil and coat with cooking spray.
Arrange chicken evenly on the prepared baking sheet; reserve marinade in the bowl.
Bake in the preheated oven for 25 minutes. Brush 1/2 of the reserved marinade onto chicken, then turn over. Bake for 15 minutes.
Turn chicken over and brush with remaining reserved marinade. Continue baking until tender and caramelized, 10 to 15 more minutes. An instant-read thermometer inserted near the bone should read at least 165 degrees F (74 degrees C). Rest chicken on the baking sheet for 5 minutes before removing to a serving platter.