Preheat the oven to 375°F (190°C) and lightly grease a 9x13-inch baking dish with clarified butter or ghee.

In a large skillet, heat olive oil and sauté the diced red onions for about 5–7 minutes until translucent and slightly golden.

Add minced garlic and crushed red pepper flakes to the onions and cook for an additional minute.

Pour in the dry red wine and let it simmer for 2–3 minutes to deglaze the pan.

Slice the butternut squash, russet potatoes, and zucchini into even rounds, about ¼ inch thick.

Layer the sliced butternut squash, russet potatoes, zucchini, and diced tomatoes in the greased baking dish.

Drizzle the sautéed onion mixture evenly over the layered vegetables.

Sprinkle fresh lemon juice, herbs de Provence, sea salt, and coarsely ground pepper generously over the vegetable layers.

Combine the shredded Gruyere, panko bread crumbs, and melted butter in a mixing bowl, then spread evenly over the top.

Bake in the preheated oven for 45 minutes until golden brown and tender.

Allow to cool for about 10 minutes before slicing and serving.