Preheat oven to 425°. Grease a 13" x 9" baking pan or 2 (8" x 5") casserole dishes with butter.
In a large pot of boiling salted water, cook pasta, stirring occasionally, until slightly firmer than al dente, about 2 minutes less than package directions. Reserve 4 cups pasta water, then drain. If there isn’t enough pasta water remaining, add water or milk to reach 4 cups liquid.
In same pot over medium heat, melt butter. Whisk in flour and cook, whisking constantly, until butter begins to foam and turns golden brown, about 4 minutes. Slowly whisk in reserved pasta water to avoid lumps. Add cream cheese and whisk until smooth.
Stir in chile (if using) and adobo sauce and cumin; season salt and pepper. Bring to a simmer, whisking constantly. Gradually add cheddar and Monterey Jack cheeses, about 1/2 cup at a time, whisking until each addition is melted and smooth before adding the next. Add pasta; season with salt and pepper and toss to combine. Transfer mixture to prepared pan.
Place pan on a foil-lined baking sheet and cover pan with foil. Bake for 30 minutes, remove foil, and continue to bake for until cheese is bubbling, about 10 minutes more. Top with avocados, jalapeños, and cilantro.
