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For the onion infused milk: Place the diced onions in a baking dish with the dried thyme. Cover with plastic wrap. In a small opening with a hand-held smoking gun, use about 2 small bowls worth of wood chips to fill the baking dish with smoke. Allow the onions and thyme to sit for 15 minutes before releasing the smoke.
For the smoked hoisin brisket: Rub the spice rub all over the brisket, and then let the brisket sit, covered, in the refrigerator for 12 hours.
Preheat a smoker with hickory wood to 225 degrees F. Smoke the brisket for 14 hours. Let cool, and then chop the brisket into 2-inch chunks while working the fat from the brisket back into the meat. Mix the chopped brisket with the hoisin sauce to coat.
For the smokey bechamel: Melt the butter in a braising pot. Add the flour slowly to the hot butter while whisking constantly and cook the roux for 5 minutes. Slowly add the onion-infused milk while stirring until the bechamel reaches desired consistency. Stir in the cheeses until completely melted.
For assembly: Preheat the oven to 400 degrees F. Boil the penne in a large pot until al dente. Drain and return to the pot. Fold the bechamel into the cooked pasta. Layer the pasta and 2 pounds of the brisket in baking dishes, stopping 1/2 inch from the top. Sprinkle with the panko. Bake until golden brown, and then garnish with fried leeks.