Bring a large pot of water to boil for the pasta.
For the queso sauce, in a medium saucepan, melt the butter over medium. Add the shallots, garlic and jalapeno. Cook, stirring often, until softened, about 3 minutes; season with salt and pepper. Stir in the cornstarch, then add the milk. Bring to a bubble, then add the cream cheese, stirring until it melts, 3 to 5 minutes. Add both cheddars and stir in a figure-eight motion until melted, about 5 minutes. Stir in the canned chiles and reduce the heat to low.
Salt the boiling water. Add the pasta; cook to al dente.
Stir the mustard into the queso sauce and remove from the heat. Drain the pasta and toss with the sauce. Top with the pico de gallo.