Cook pasta according to package directions; drain.
Meanwhile, sauté onion and jalapeno pepper in butter in a Dutch oven over medium-high heat until tender.
Reduce heat to medium-low.
Stir in flour until combined.
Gradually stir in milk and liquid smoke if desired.
Bring to a boil; cook and stir for 2 minutes or until thickened.
Reduce heat to low.
Gradually stir in cheddar and gouda until melted.
Stir in the pasta, chicken, barbecue sauce and cayenne pepper; heat through.
Remove from the heat.
Season with salt to taste.
Garnish with green onions, cilantro and additional barbecue sauce.