Preheat oven to 400℉ and line a large baking sheet with parchment paper or aluminum foil.
Toss the squash and olive oil together on the prepared sheet pan. In a small bowl, combine the dried thyme, salt, dried sage, paprika, ground cinnamon, and ground nutmeg. Sprinkle the herbs and spices over the squash and gently toss to coat the squash with the herbs.
Transfer the butternut squash to the oven and bake for 10 minutes, gently toss and continue to bake until fork-tender, approximately 10-15 minutes more.
In the meantime, cook the bacon in a large skillet over medium heat until crispy. Drain most of the fat from the pan, leaving only about 2 tablespoons.
Add the kale and cook until it is tender, stirring often, about 5 minutes. Then, stir in the chopped pecans, maple syrup, salt, and cinnamon. Remove from heat and allow it to cool for at least 15 minutes.
Combine the breadcrumbs and brown sugar in a medium bowl, then stir in the melted butter and set aside.
In a large bowl, toss together the roasted butternut squash and bacon mixture, along with the chopped apple and ¾ of the cheese.
Grease a large 9x13-inch casserole dish and pour the filling into the pan. Arrange the remaining cheese pieces around on top, then sprinkle the breadcrumb mixture on top.
Transfer to the oven and bake for 25-30 minutes or until the top turns golden and crispy. Garnish with fresh oregano if desired.