Place an aluminum foil–lined rimmed baking sheet on middle oven rack. Preheat oven to 500°F.
Combine squash, poblano, onion, garlic, and oil in a large bowl. Add cumin, paprika, cinnamon, salt, and cayenne; toss to coat. Carefully remove pan from oven; coat with cooking spray. Spread squash mixture on pan. Roast at 500°F for 10 minutes. Stir vegetables; turn on broiler. Broil on middle rack until squash is tender, about 5 minutes. Remove from oven; transfer vegetables to a bowl, and peel garlic cloves. Discard foil; line pan with new foil, and return to oven. Reduce oven temperature to 475°F.
Bring milk and flour to a boil in a saucepan over high, whisking constantly. Cook, whisking constantly, until reduced to about 3/4 cup, 5 to 6 minutes. Remove from heat; let cool 10 minutes.
Roll dough out into a 12-inch oval on a floured surface. Coat prepared baking sheet with cooking spray. Place dough on baking sheet; prick all over with a fork. Bake at 475°F until dry, about 4 minutes. Remove from oven; spread milk mixture over pizza, leaving a 1/2-inch border. Top with vegetables and 1/4 cup cheese. Bake at 475°F 10 to 12 minutes. Top with cilantro, pepitas, and remaining 1/2 cup cheese.