Preheat the oven to 425°F (220°C). Line a large rimmed sheet pan with parchment paper.
Whisk the olive oil, maple syrup, Dijon mustard, apple cider vinegar, garlic, thyme, rosemary, smoked paprika, salt, and black pepper. Transfer 2 tablespoons to a separate clean bowl for finishing.
Spread the butternut squash, Brussels sprouts, and red onion on the prepared pan. Toss with about half of the remaining glaze and arrange in a single layer.
Pat the chicken thighs very dry. Coat them with the rest of the glaze and nestle them skin-side up among the vegetables, leaving space around each piece.
Roast for 20 minutes without turning the chicken.
Remove the pan, stir the vegetables, and add the apple wedges. Return the pan to the oven for 15 to 20 minutes.
Cook until the chicken reaches at least 165°F (74°C) in the thickest part, the squash is fork-tender, and the vegetables are browned. Broil for 1 to 2 minutes if deeper color is desired, watching closely.
Brush the chicken lightly with the clean reserved glaze. Rest for 5 minutes, garnish with fresh thyme if desired, and serve with the roasted vegetables and apples.