Combine broccoli, red bell peppers, and yellow onion in a large bowl. Add olive oil, juice of 2 limes, and 1/2 teaspoon salt; toss to coat. Spread vegetables onto a baking sheet.
Roast vegetables, stirring 1 or 2 times, in the preheated oven until edges begin to blacken, about 30 minutes. Remove from oven and cool slightly.
Fill a large pot with water and 1/2 teaspoon salt; bring to a boil. Stir in penne and return to a boil. Cook pasta uncovered, stirring occasionally, until cooked through but still firm to the bite, about 11 minutes; drain.
Blend avocados, juice of 2 limes, garlic, and 1/2 teaspoon salt in a food processor or blender until sauce is smooth, scraping down sides as needed. Add 1/2 cup chopped cilantro and pulse until just incorporated.
Gently toss pasta, roasted vegetables, and sauce together in a large bowl. Garnish with cherry tomatoes, cilantro stems, sea salt, and black pepper.
