Preheat oven to 425°. Rub squash with 2 tsp. oil and set on a baking sheet. Roast squash, turning once, until tender when pierced with a fork, about 20 minutes.
Meanwhile, spread pumpkin seeds on a rimmed baking sheet. Drizzle with remaining 1 tsp. oil and the table salt, stirring to coat. Bake until toasted, about 5 minutes.
Put squash on a serving plate. Drizzle with honey, then sprinkle with pomegranate seeds, toasted pumpkin seeds, and sea salt.
Mix butter and cayenne and serve on the side for guests to drizzle over squash.
Make ahead: Up to 2 days ahead through step Rewarm squash in oven 5 minutes, then continue with recipe.