For the apple and red chile mole: Heat the oil in a medium Dutch oven over medium-high heat. Add the garlic and onions and cook until slightly softened, about 3 minutes. Add the ancho powder, allspice, chiles de arbol, cloves, apples and cinnamon sticks and some salt and pepper. Cook, stirring, for about 3 minutes. Stir in the chipotle puree, then the almonds, tortilla chips and raisins. Add the chicken stock, 1 cup of the apple cider, the tomatoes and cider vinegar. Bring to a boil, reduce the heat and simmer, stirring occasionally, until slightly thickened and reduced, about 15 minutes.
Stir in the brown sugar, honey and maple syrup and cook, stirring, another 10 minutes. Stir in the chocolate to melt. Remove the cinnamon sticks and discard. If the mixture seems too thick to blend easily, add a little extra cider. Transfer the mixture to a blender and, starting on very low speed, blend until smooth. Again, if the sauce seems too thick, thin it with a bit more cider. Return the sauce to the pot and cook very gently for another 10 minutes. Taste and adjust the seasoning as needed. Cover to keep warm while you cook the chicken.
For the roasted cider-glazed chicken: Preheat the oven to 400 degrees F.
Season the chicken on both sides with salt and pepper. Heat the oil in a large cast-iron skillet over medium heat until it begins to shimmer. Working in batches if necessary to avoid crowding the pan, add the chicken skin-side down and cook until the fat renders and the skin begins to turn golden brown. Turn, cook for a few minutes to start browning the second side, and then transfer to the oven.
While the chicken cooks, whisk together the cider, honey and thyme in a small saucepan over medium heat. Bring to a boil, and then remove from the heat.
After the chicken has cooked for about 10 minutes, brush with the glaze. Continue to cook, brushing with glaze occasionally, until the chicken reaches 160 degrees F on an instant-read thermometer, about 15 minutes total for the breasts, 20 to 25 minutes for the thighs and drumsticks.
Ladle some of the mole onto a platter and top with the chicken pieces. Spoon some more mole over the top, sprinkle with scallions and serve.
When blending hot liquid, first let it cool for five minutes or so, then transfer it to a blender, filling only halfway. Put the lid on, leaving one corner open. Cover the lid with a kitchen towel to catch splatters, and pulse until smooth.