Preheat oven to 350°F and grease an 8x8-inch baking dish.
Cook the pasta in boiling water for about 7 minutes, or until just shy of al dente. Reserve about 1/4 cup pasta water, then drain.
Melt the butter in a large saucepan over medium heat. Stir in the flour until smooth and cook for about 1 1/2 minutes, stirring occasionally.
Stir in the salt, black pepper, garlic powder, and onion powder.
Slowly whisk in the milk, making sure the mixture stays smooth.
Add the chopped chipotle peppers, adobo sauce, and cilantro. Increase heat slightly and cook, stirring often, until the sauce thickens enough to coat the back of a spoon and begins to simmer.
Reduce heat and simmer for about 2 minutes, then remove from heat.
Gradually stir in most of the pepper Jack, and cheddar, reserving a little cheese for the top. If the sauce becomes too thick, add a splash of reserved pasta water until smooth and creamy.
Add the drained pasta and stir until evenly coated.
Transfer to the prepared baking dish. Sprinkle with the reserved cheese and panko breadcrumbs.
Bake uncovered for about 15–20 minutes, until bubbling around the edges and lightly browned on top.
Let rest for about 5 minutes before serving. Garnish with extra cilantro if desired.