Preheat the oven to 375°F. Butter a large gratin dish.
Cook the pasta in salted boiling water until al dente. Drain well and transfer to a large bowl.
Add the sausage, fresh jalapeños and pepperoncini to the pasta. Set aside.
Melt 3 tablespoons butter in a saucepan over medium heat. Add the onion and cook, stirring often, until softened and translucent, about 8 minutes.
Add the flour and cook, stirring constantly, for 3 minutes. While stirring, slowly add the milk and cook gently until thickened, about 3 minutes. Season to taste with salt and pepper.
Set aside about 1 cup of the chopped cheese. Add the remaining cheese to the sauce and stir until completely melted. Pour the cheese sauce over the pasta and sausage and stir gently until completely coated. Transfer the pasta to the buttered gratin dish.
Melt the remaining 3 tablespoons butter then pour over the bread crumbs and stir to combine. Stir in the reserved cheese. Sprinkle the bread crumb mixture evenly over the pasta.
Bake the pasta until bubbling and the crumbs are golden brown, about 30 minutes. Let rest for 5 minutes before serving.