Preheat oven to 375°F. Bake peppers in a baking dish 10 minutes to soften slightly.
Mix quinoa, corn, beans, tomatoes, cream cheese, 1 cup cheddar, garlic powder, onion powder, salt, and pepper in a large bowl until cream cheese is incorporated.
Remove peppers; fill generously with mixture, packing gently.
Top with remaining cheddar and half the bacon.
Cover dish with foil; bake 20 minutes. Uncover; bake another 5 minutes until cheese melts and bubbles.
Serve topped with sour cream, remaining bacon, and chives.