Preheat oven to 375 degrees. Spray a 9” x 9” x 2” baking dish with non-stick cooking spray; set aside.
In a large pot, bring 3 - 4 quarts of water to a rolling boil. Add pasta and salt to taste and cook according to package directions to al dente. Drain; set aside.
Meanwhile, in a large skillet, heat olive oil over medium heat. Add onion and jalapeno pepper; cook until softened, approximately 3 - 4 minutes, drain; set aside.
In a large dutch oven, melt the butter over medium heat. Add the garlic and cook for 1 minute. Add the flour and cook for 2 minutes. Whisk in the milk, beer, salt, pepper and nutmeg and cook until mixture begins to boil and thicken, approximately 5 - 8 minutes, stirring constantly. Add in the chipotle gouda cheese, cheddar cheese and queso quesadilla cheese and stir until cheeses have fully melted and sauce is smooth; remove from heat. Add in the reserved pasta and mix to combine. Add in the reserved onion/pepper mixture and mix to combine.
Place macaroni and cheese in prepared baking dish and top evenly with the tortilla chips. Place in preheated oven and cook for 25 - 30 minutes until heated through and bubbly. Let rest for 5 minutes.