Place potatoes in a large saucepan and cover with water. Set over moderate heat and bring to a boil. Reduce heat; cook, uncovered, for 10-15 minutes or until fork tender.
Place pumpkin in a separate large saucepan and cover with water. Set over moderate heat as well, and bring to a boil. Reduce heat; cook, uncovered, for 20-25 minutes or until tender.
Meanwhile make the topping. Set a large skillet over medium heat with 3 tablespoons butter. Once melted, add the onion and garlic and cook until softened, about 3 to 5 minutes. Season with salt, pepper, and crushed red pepper flakes. Stir in the cubed bread and cook, stirring often, until golden brown and just beginning to brown. Add the pepitas and sage and cook for another minute or so. Give it a taste and adjust seasoning accordingly. Keep warm.
Drain potatoes and return to the pot to cook off the moisture. Mash potatoes, adding 1/4 cup milk, 4 tablespoons butter, 1/2 teaspoon salt, and 1/4 teaspoon black pepper. Add additional milk if needed to reach desired consistency. Keep warm over very low heat.
Drain pumpkin and return to the same pot. Mash pumpkin, gradually adding the remaining 4 tablespoons butter, 1/2 teaspoon salt, 1/4 teaspoon pepper, spices and enough remaining milk to reach desired consistency.
Layer the mashed potato and pumpkin, alternating dollops between the two, in a large serving dish or platter. Top with the herby bread mixture and serve immediately. Enjoy!