Heat the oven to 375° and coat a standard 12-cup muffin tin with cooking spray. Cook the macaroni according to the package instructions, drain it, and transfer it to a large bowl. Add the cheddar and 1/2 cup of the Parmesan and stir until the cheese has melted. In a separate bowl, lightly beat the eggs, then whisk in the milk and ricotta. Combine the egg and pasta mixtures. Stir in the broccoli, scallions, nutmeg, mustard, salt, and pepper. Evenly divide the mixture among the muffin wells.
In a small bowl, stir together the panko, melted butter, and remaining Parmesan. Evenly divide the mixture among the macaroni cups and use your fingers to press and pack the contents of each well. Cook the cupcakes until they're set and the tops are golden brown, about 15 minutes. Let the cupcakes cool for 5 minutes before unmolding them.