Bring a large pot of water to a boil. Salt the water and cook the penne until al dente, about 8 minutes, adding the cauliflower during the last 4 minutes of cooking. Drain and return pasta and cauliflower to the pot.
Meanwhile, in a medium skillet over medium-low, heat the EVOO, two turns of the pan. Add 1 tbsp. of the butter. Once it foams, add the shallots and garlic. Season with salt, pepper, the thyme and rosemary. Cook, stirring occasionally, until shallots are light golden, about 20 minutes. Stir in 1/2 cup of the stock.
Preheat the broiler. In a medium saucepan, melt the remaining 4 tbsp. butter over medium heat. Whisk in the flour, nutmeg and dry mustard and cook for 1 minute. Whisk in the milk and the remaining 1/2 cup stock, then stir in the cheese using a figure-8 motion. Cook over medium-high heat until thick enough to coat the spoon, 2 to 3 minutes. Remove from the heat.
Add the shallot mixture and sauce to the pasta pot. Stir to combine. Transfer to a 9-by-13-inch baking dish; top with the parmigiano-reggiano. Broil until browned and bubbling, 1 to 2 minutes. Let sit for 10 minutes before serving.