Preheat the oven to 400°F.
In a baking dish, toss together the butternut squash, parsnips, olive oil, sage, 2 teaspoons salt, 1 teaspoon pepper, and thyme.
Bake until tender, stirring every 20 minutes, for about 1 hour to 1 hour 20 minutes.
Meanwhile, cook the bacon in a skillet until crisp, about 10 to 12 minutes. Transfer bacon to a plate and crumble.
Add onions to the bacon drippings and cook until softened, about 25 to 35 minutes. Stir in kale, butter, vinegar, remaining ½ teaspoon salt, and ½ teaspoon pepper. Cover and cook until kale is wilted, about 1 to 2 minutes.
Add the kale mixture and bacon to the butternut squash mixture in the baking dish and mix gently.
Sprinkle with cheese and bake until melted, about 5 minutes.
Sprinkle with almonds and garnish with sage and thyme leaves.