Heat water for pasta, salt water and cook pasta to al dente.
While pasta water comes to boil, heat the EVOO, one turn of the pan, in a deep skillet over medium-high heat. When EVOO is hot, add bacon and crisp, 5-6 minutes. Remove with a slotted spoon and drain off some of the fat if you have more than 2-3 tablespoons. Add onions and cook for 10 minutes, until soft and beginning to caramelize. Add wine and cook out, 1 minute.
While onions cook, heat a saucepot over medium heat. Add butter, melt, then whisk in flour. Cook for 1 minute, then whisk in chicken stock and milk and bring to a bubble. Thicken for a few minutes, then season with salt and pepper. Melt in cheese, stirring it in a figure eight motion with 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.