Preheat the oven to 400°F and place squash halves cut-side down on a parchment-lined baking sheet. Brush cut sides with 1 tablespoon olive oil and sprinkle with 1/4 teaspoon salt and black pepper.
Roast squash for 35-40 minutes until tender when pierced with a fork.
Heat remaining 1 tablespoon olive oil in a large skillet over medium heat. Add diced onion and cook until softened, about 3 minutes.
Add minced garlic, diced red bell pepper, and jalapeño to the skillet; cook 4-5 minutes until vegetables are soft.
Add kidney beans, black beans, diced tomatoes, vegetable broth, chili powder, cumin, smoked paprika, remaining 1/4 teaspoon salt, black pepper, and 1 tablespoon hot honey. Stir and bring to a gentle simmer.
Stir in uncooked elbow macaroni, cover the skillet, and cook for 8-10 minutes, stirring occasionally, until pasta is al dente. Add extra broth or water if mixture thickens too much.
Remove skillet from heat and stir in shredded cheddar cheese until fully melted and creamy.
Flip roasted squash halves cut-side up when cool enough. Spoon generous portions of chili mac filling into each half.
Drizzle additional hot honey over the stuffed squash and garnish with chopped fresh cilantro before serving.