In a large bowl, combine the milk, garlic, shallot, thyme, ½ of the parmesan, ½ teaspoon salt and pepper. Add the squash and toss to coat. Spray a medium oven-safe casserole dish with cooking spray. Transfer squash mixture to casserole dish and set aside.
In a medium microwave safe bowl, melt butter. Add breadcrumbs, remaining parmesan, ¼ teaspoon salt, and pepper. Evenly spread breadcrumb mixture over squash, cover with foil and bake for 45 minutes. Uncover and broil 2-3 minutes to brown top (watch carefully because it browns quickly!)