In a large saucepan, melt the butter over medium heat. Add the onion and a pinch of salt. Cook, stirring, until the onion is soft and translucent, 5 to 7 minutes. Stir in the paprika, cayenne, nutmeg, allspice, and a few turns of pepper and cook for 2 minutes more. Increase the heat to medium-high and add the flour, whisking until combined, then cook for 1 minute. Add half the milk, whisking continuously until thickened, about 5 minutes, and then repeat with the other half of the milk. Add the Brie and Gruyère and stir until the cheese is melted. Remove from the heat and add the pasta.