Heat milk in a saucepan until it is steaming - don't boil - so use a low flame. In another large saucepan, melt butter. Add flour to melted butter and whisk together over medium heat cooking for about two - three minutes. You want to be able to smell a sort of nuttiness to it, cooking out the raw flour taste - and this is called a roux.
To the roux, SLOWLY pour in the hot milk whisking constantly to incorporate. Add your pinch of ground nutmeg. Continue cooking this until you see a few bubbles pop up and it is thickened.
Remove the bechamel from the heat and whisk in the creme fraiche first. Next whisk in both cheeses until fully incorporated. Last whisk in the Guinness. Salt and pepper the sauce to taste.
Preheat your oven to 400 and grease a baking dish, a pretty big one. Add your al dente noddles to the dish and pour the cheese sauce over, careful not to spill all over and waste some of that glorious sauce. Toss together and spread across the pan.
In a saute pan melt the butter over medium heat, and add the garlic and thyme and cook for a minute, just until fragrant. Add the breadcrumbs and toast ever so slighty, combining with the garlic and thyme. Add a little salt and pepper to taste. Pull the thyme twigs out.
Top the mac n cheese with the breadcrumb mixture and bake in the oven until bubbly and brown. If you assemble ahead of time and refrigerate, it will take longer to bake, if you assemble and throw right in oven already hot, it will not take that long, so pay attention to the the dish in the oven.