Add the broccoli to boiling salted water and cook 2 minutes, then drain and plunge into a bowl of ice water. Remove and set aside.
Put the panko in a small bowl. Melt the butter in a medium saucepan over medium-high heat. Pour 1 tablespoon of the butter over the panko and mix it well to coat; stir in 1 tablespoon Parmesan and set aside.
Stir the garlic into the saucepan and cook, 30 seconds. Add the flour and stir to incorporate. Gradually whisk in the milk and bring to a simmer, then cook until slightly thickened, about 1 minute. Take off the heat and add the Cheddar, Gruyere, the remaining 3 tablespoons Parmesan, then the nutmeg and cayenne, stirring until smooth. Stir in the broccoli and tomatoes and season with salt to taste.
Add the gnocchi to the sauce and stir to coat. Transfer to an 8-inch square baking dish and sprinkle with the panko. Bake until bubbling and golden brown in spots, 25 to 30 minutes.