Preheat the oven to 400°F/200°C.
In a large bowl, toss all the vegetables with olive oil, chipotle powder, salt, black pepper, garlic powder, paprika, and cayenne until evenly coated. Transfer to a large baking dish.
Combine the walnuts, honey, olive oil, thyme, and chipotle powder in a small bowl. Spread the glazed walnuts evenly over the vegetables.
Cover the dish with foil and roast for 30–40 minutes, until the vegetables are nearly tender.
Remove the foil and roast for another 30–35 minutes, or until fork-tender and lightly caramelized. Oven times may vary.
Garnish with additional fresh thyme and flaky sea salt before serving.