Preheat the oven to 400 degrees F (200 degrees C).
Place cubed butternut squash and chopped onion in a large baking pan. Drizzle with olive oil and season lightly with salt and pepper. Toss to coat.
Roast in the preheated oven until tender, about 20 minutes.
Meanwhile, heat a pan over medium-high heat. Add soy chorizo; cook and stir until browned, 5 to 7 minutes.
Reduce oven heat to 350 degrees F (175 degrees C). Stir the roasted squash, onion, chorizo, and 2 tablespoons cilantro together in a medium bowl.
Stir salsa and yogurt together in another bowl. Pour a thin layer over the bottom of a 9x13-inch baking dish or two 8-inch square dishes. Dip 1 tortilla into the sauce; fill with about 1/3 cup of the squash mixture and 1 tablespoon cheese. Roll up and place seam-side down in the baking dish. Repeat until all the squash mixture is used up. Cover enchiladas with remaining salsa mixture and cheese.
Bake in the preheated oven until cheese has melted is is starting to brown in places, about 30 minutes. Let cool for 5 minutes. Garnish with avocado and remaining cilantro.
