Boil pasta until al dente in large pot of salted water. Drain pasta and set aside to dry.
Return pot to stove and melt half of butter over moderate heat. Add in jalapeño and onion and cook, stirring occasionally, until onion is golden-brown and softened, about 15 minutes.
Add 3-4 drops of liquid smoke and stir.
Melt remaining butter with jalapeños and onions, then stir in flour, a bit at a time, until completely combined. Continue to stir until flour turns golden and onions and jalapeños are well-coated, about 2 minutes. Slowly stir in milk and continue to stir until sauce is thick enough to coat the back of a spoon. Mix in salt.
A handful at a time, stir in cheddar and gouda, making sure each handful is melted entirely before adding in next. Add barbecue sauce and cayenne pepper and mix until well-combined. Remove from heat and add cooked pasta and chicken breast. Mix well.
Garnish with cilantro and green onion and drizzle with BBQ sauce. Serve warm.