Preheat oven to 400°. Coat a 13"-by-9" baking dish with nonstick spray.
In a medium skillet over medium heat, cook bacon, stirring occasionally, until crisp, about 5 minutes.
Transfer bacon and 2 tablespoons bacon fat to a large bowl. Discard remaining bacon fat or save for another use. Add squash, onion, leek, kale, garlic, sage, thyme, salt, and black pepper to bowl. Toss to combine.
Arrange vegetable mixture in an even layer in prepared dish. Bake until a knife easily inserts into squash, about 30 minutes.
Top casserole with mozzarella and cheddar in an even layer. In a small bowl, mix panko, Italian seasoning, and oil, then sprinkle over cheese.
Continue to bake until cheese is melted and bread crumbs are golden brown, 10 to 15 minutes more.
