Salt chicken inside and out, tie legs together and trim wing tips. Refrigerate several hours or overnight uncovered or on the counter for at least 1 hour.
Preheat oven to 425°F.
In a large mixing bowl, toss squash, onions and apples with EVOO to coat lightly, half the thyme, salt and pepper.
Combine chipotle and honey or maple syrup and a drizzle of oil. Slather bird with sauce and season with pepper and thyme.
Heat a cast-iron skillet over medium to medium-high heat. Add bacon and cook to render fat. Remove pan from heat, add vegetables to the pan and set chicken on top. Transfer skillet to oven and roast 1 hour to an internal temperature of 160°F on thermometer.
Let chicken rest 15-20 minutes.
Remove vegetables to platter and place pan on heat, whisk in cider and beer, and cook to reduce pan drippings by half.
Carve chicken into 8 pieces and serve with squash, apples and onions and cider-beer jus.