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Preheat oven to 375°F. Bring a large pot of salted water to a boil over medium-high. Cook pasta 2 minutes less than package directions for al dente, 6 to 8 minutes. Drain and set aside.
Melt 3 tablespoons butter in a Dutch oven over medium. Whisk in flour; cook, whisking constantly, until mixture is lightly browned, about 30 seconds. Gradually add milk, whisking constantly. Cook, whisking often, until mixture is thick enough to coat the back of a spoon, 3 to 4 minutes.
Remove from heat. Gradually whisk in cheddar, mustard, thyme, 1 ¾ cups Gruyère, and 2 teaspoons salt until melted and smooth. Stir in pasta and Frenched onions, reserving ¼ cup Frenched onions for topping. Transfer mixture to an 8- x 8-inch baking dish.
Microwave remaining 1 ½ tablespoons butter in a medium microwavable bowl until melted, about 30 seconds. Add bread pieces and remaining ¼ teaspoon salt; toss to coat. Sprinkle bread pieces, reserved ¼ cup Frenched onions, and remaining ¼ cup Gruyère evenly over pasta mixture.
Bake, uncovered, until mac and cheese is bubbly and golden, about 25 minutes. Let cool 5 minutes before serving. Garnish with thyme leaves and black pepper.