Preheat and prep: Heat your oven to 400°F (200°C).
Line a baking sheet with parchment for easy cleanup.
Roast the squash: Halve the spaghetti squash lengthwise and scoop out the seeds. Brush the cut sides with 1 tablespoon olive oil and season with salt and pepper. Place cut-side down on the baking sheet and roast for 35–45 minutes, until the skin gives slightly when pressed and the strands pull apart easily with a fork.
Shred the squash: Let the squash cool for 5 minutes.
Use a fork to gently scrape the flesh into spaghetti-like strands, keeping the strands in each half so they form “boats.” Leave a thin layer of squash in the shell to help it hold its shape.
Mix the chicken: In a bowl, combine shredded chicken, BBQ sauce, smoked paprika, garlic powder, onion powder, and apple cider vinegar if using. Taste and adjust salt, pepper, or vinegar for balance.
Combine with squash: Drizzle the remaining 1 tablespoon olive oil over the squash strands and toss lightly in the shells. Divide the BBQ chicken mixture between both squash halves and gently mix to distribute.
Top with cheese: Sprinkle mozzarella and cheddar evenly over the tops.
Add a few jalapeño slices if you like a kick.
Bake to melt: Return to the oven for 10–12 minutes, until the cheese is melted and bubbling. For extra color, broil for 1–2 minutes, watching closely.
Finish and serve: Garnish with green onions and cilantro. Serve hot, straight from the boats, or scoop into bowls.