Preheat oven to 350°F and butter 9 1/2 x11-inch baking pan or 8 individual ramekins. Cook macaroni according to the package directions. Drain and set aside.
While macaroni is cooking, heat 1 tablespoon olive oil in sauté pan. Sauté onions until caramelized, at least 30 minutes; remove from pan. In a saucepan, warm milk over low heat.
Heat 1 tablespoon butter in pan used for onions; add mushrooms and sauté until fully cooked, about 7-10 minutes. Add salt and pepper to taste.
To make cheese sauce, add 4 tablespoons butter to a medium-sized saucepan and heat over medium heat. Whisk in 4 tablespoons flour and stir about 1 minute. Add thyme, salt and pepper and cook for another minute, stirring constantly. Slowly pour in the warm milk and simmer until sauce is thick, stirring constantly. Add truffle oil and Dijon mustard and stir well. Remove from heat and stir in shredded Grand Cru.
To assemble, pour about 1/2 cup of the cheese sauce in the baking pan—just enough to coat bottom. Add layer of macaroni, layer of onions and layer of mushrooms (1/2 of each). Pour about half of remaining cheese sauce on top, and repeat layer with remaining onions, mushrooms and cheese sauce.
In small bowl, mix shredded cheddar and panko. Sprinkle mixture on top of casserole. Cook for 20-30 minutes, or until top is golden and bubbly.
If fresh shitakes are not available, you may substitute dried. Add to the milk while you warm it and soak until mushrooms are rehydrated. Strain, reserving milk, and sauté with creminis. This will also infuse the sauce with smoky mushroom flavor.