Heat water for pasta, salt water and cook pasta to al dente.
While pasta water comes to boil, heat extra-virgin olive oil, 1 turn of the pan, in a deep skillet over medium-high heat. When oil is hot, add bacon and crisp, 5 to 6 minutes. Remove with a slotted spoon and drain on paper towels. Add onions and cook 10 minutes until soft and beginning to caramelize. Add wine and cook out, 1 minute.
While onions cook, heat a sauce pot over medium heat. Add butter, melt and whisk in flour. Cook 1 minute then whisk in stock and milk and bring to a bubble. Thicken a few minutes then season with salt and pepper. Melt in cheese stirring it in a figure-8 motion with a wooden spoon. Add nutmeg and mustard and adjust salt and pepper.
Drain pasta, toss with onions and stir in cheese sauce to coat. Top with crispy bacon and serve.