With a sharp paring knife, core the Brussels sprouts and separate the leaves; place in a large bowl.
Heat a large pot of water to boil and salt the water. Parboil the leaves to tender crisp, 2 minutes. Remove with a spider, drain and cool. Dry the leaves on a kitchen towel. Add more water to fill the pot back up for the pasta, return to a boil.
Heat a saucepot over medium heat; add the EVOO and brown the bacon. Remove and drain. Pour off most of the drippings, then add the butter and melt. Add the garlic and onions, stir 5 minutes. Add a little salt and pepper, then stir in the flour for 1 minute. Whisk in the wine to deglaze the saucepot. Whisk in the stock and then the milk. Season with a little bit of nutmeg. Thicken the sauce to coat the back of a spoon. Reduce the heat to low.
Boil the pasta to just shy of al dente, 5 to 6 minutes, drain.
Stir two-thirds each of the Cheddar, gruyere and Parmigiano-Reggiano into the sauce in a figure-eight motion. Drain the pasta, then toss with the Brussels sprouts, bacon and sauce, and pour into a baking dish. Top with the remaining cheese. Cool and store for a make-ahead meal, or bake to serve. Place into the oven and bake until heated through and bubbly and brown on top.