Bring a large pot of salted water to a boil. Add the broccoli and cook until bright green and crisp-tender, 3 to 4 minutes. Remove to a plate with a slotted spoon; let cool. Return the water to a boil. Add the pasta and cook as the label directs. Reserve 1 cup cooking water, then drain.
Whisk the eggs, evaporated milk, the reserved cooking water, the Mexican cheese, 1/2 cup parmesan, the mustard, nutmeg, 1/2 teaspoon salt and a few grinds of pepper in a large saucepan. Cook over medium-low heat, whisking constantly, until the mixture starts to thicken and bubble, 6 to 8 minutes. Stir in the pasta and broccoli until coated. Transfer the mixture to a 3-quart baking dish and top with the tomatoes.
Preheat the broiler. Combine the remaining 1/4 cup parmesan, the breadcrumbs and melted butter in a small bowl; sprinkle over the macaroni and cheese. Broil, rotating the pan, until the topping is golden brown, 4 to 5 minutes.