Preheat oven to 400°F. Cook pasta according to package directions. Drain, reserving ⅓ cup of the water for later. Grease 13- x 9-inch baking dish.
Melt butter in large skillet set over medium heat; remove 2 tbsp melted butter and toss with bread crumbs. Set aside.
Add onion, garlic, thyme, pepper and chili flakes to remaining butter in skillet; cook for about 3 minutes or until softened. Stir in flour. Cook, stirring, for 2 to 3 minutes or until smooth
Slowly whisk in milk and Lobster Base; bring to boil, whisking constantly. Reduce heat to medium-low; cook, stirring constantly, for about 10 minutes or until thickened slightly. Remove from heat.
Stir in 2 cups cheese until melted. Stir in pasta, reserved cooking liquid, lobster, lemon juice and half of the chives. Transfer to prepared baking dish. Sprinkle bread crumb topping and remaining cheese over top.
Bake for 12 to 15 minutes or until golden and bubbly. Let stand for 10 minutes before serving. Sprinkle with remaining chives.