Dry the pot and add the butter over medium heat. Add the chopped onion and jalapeño and cook, stirring occasionally, until softened, about 6 minutes. Add the flour and salt, and cook, stirring occasionally, until the flour has darkened slightly in color, about 2 minutes. While whisking constantly, slowly add the milk to the flour mixture until evenly combined and smooth. Cook, stirring occasionally, until the mixture comes to a simmer and thickens slightly, about 8 to 10 minutes. Add the salsa and cheeses and stir until completely melted and the sauce is smooth. Stir in the pasta, pickled jalapeños and green chiles and stir to combine. Taste and season with salt and pepper as needed.