Bring large pot of water to boil. Add pasta and cook according to package directions. Drain and set aside.
Meanwhile, melt 1/2 tablespoon butter in small skillet over medium-high heat. Add onion, red pepper and jalapeño pepper. Cook, stirring occasionally, until fragrant and tender, about 5 to 7 minutes. Remove from heat and set aside.
In medium saucepan, melt 4 tablespoons butter over medium-high heat. Once butter is completely melted, whisk in flour. Cook mixture, whisking constantly, until it turns light golden brown color and begins to foam, about 2 minutes. Whisk in milk until well blended. Cook mixture, whisking or stirring frequently, until it begins to bubble and thicken, about 5 minutes. Reduce heat to medium-low. Whisk in cayenne pepper, onion powder, garlic powder, salt and pepper. Add cheeses to mixture and whisk until completely melted and well incorporated. Remove from heat.
Preheat oven to 375°F. Butter 2-quart casserole dish. Return drained pasta to large pot. Add in the sautéed vegetables and cheese sauce; mix until well blended. Transfer mixture to prepared casserole dish.
Melt remaining 2 tablespoons butter in small bowl. Use food processor to pulse the bread into coarse crumbs. Add to melted butter and toss. Sprinkle crumb mixture in even layer on top of pasta. Bake 25 minutes, or until mixture is heated through and topping is golden brown. Let stand 5 to 10 minutes before serving.