Place a rack in lower third of oven; preheat to 400°F. Heat 3 Tbsp. oil3 tablespoons in a large ovenproof skillet over medium. Add onions2 and cook, stirring occasionally, until softened but not browned, 6–8 minutes. Add squash1/2 and cook, stirring occasionally, until almost tender, 8–10 minutes. Mix in thyme1 1/2 teaspoons and red pepper flakes1/2 teaspoon and transfer to a medium bowl; let cool. Wipe out and reserve skillet.