Arrange a rack in center of oven; preheat to 375°. Grease a 13" x 9" baking dish with cooking spray.

In a large skillet over medium heat, melt butter. Add onion; season with 1 tsp. salt. Reduce heat to medium-low and cook, stirring occasionally and reducing heat or adding a splash of water if onions are browning too quickly, until deeply caramelized, about 30 minutes.

Meanwhile, in a large pot of boiling salted water, cook shells, stirring occasionally, until al dente according to package directions. Drain and return shells to pot. Drizzle with oil and toss to prevent sticking.

Add wine to caramelized onions, increase heat to medium-high, and scrape up any browned bits on bottom of skillet. Stir in garlic and thyme and cook, stirring, until liquid is reduced, 1 to 2 minutes.

In a medium bowl, combine egg, ricotta, 1 cup Gruyère, and ½ cup Parmesan; season with salt and pepper. Fold in half of caramelized onions.

Carefully fill each shell with a few tablespoons egg mixture. Arrange shells in rows in prepared dish.

Sprinkle flour over remaining onions in skillet. Cook over medium-low heat, stirring, until flour is toasty smelling and pasty, about 1 minute. Pour in broth and cook, stirring constantly, until mixture comes to a boil and slightly thickens, about 5 minutes.

Pour sauce over shells, distributing onions over shells. In a medium bowl, combine panko and remaining ½ cup Gruyère and 1 Tbsp. oil. Sprinkle mixture over shells.

Cover pan and bake shells 20 minutes. Uncover and continue to bake until breadcrumbs are golden and cheese is melted, about 10 minutes more. Let cool 5 to 10 minutes in dish. Top with more thyme.