Preheat oven to 400 degrees. Make the filling: Heat oil in a large saute pan over medium-high heat. Add sausage, and cook, stirring, until golden and cooked through, 5 to 6 minutes. Transfer sausage to a paper-towel-lined plate.
Reduce heat to medium, and add shallots to drippings in pan. Cook, stirring often, until softened and translucent, about 4 minutes. Add chard, and cook, stirring frequently, until just starting to wilt, 1 to 2 minutes. Add garlic, lemon zest, and salt, and season with pepper. Cook, stirring often, until chard wilts completely, about 3 minutes. Stir in lemon juice. Transfer to a colander to drain.
Make the bechamel: Melt butter in a medium saucepan over medium heat. Add onion, salt, and red-pepper flakes, and cook, stirring occasionally, until onions are slightly translucent, about 5 minutes. Stir in flour and cook, stirring, for 1 minute. Whisk in milk, a little at a time, until incorporated. Bring to a boil, stirring often, then reduce heat to low. Simmer, stirring gently and often, until thickened and creamy, about 10 minutes. Remove from heat. Place a piece of parchment flush against the surface of sauce to prevent a skin from forming.
Place 8 baking dishes that are 7 inches across and 1 1/2 inches deep on rimmed baking sheets. Spread 3 tablespoons of bechamel in each dish, and top with a noodle. Spread 3 tablespoons chard mixture evenly in each dish, then divide 1/2 of the sausage mixture among dishes (about cup each). Top each dish with 2 tablespoons bechamel, then a noodle. Repeat once with chard, sausage, bechamel, and another noodle. Top each with 2 tablespoons of bechamel. Sprinkle each with 2 tablespoons fontina.
Bake until cheese is golden brown and sauce is bubbling, 30 to 35 minutes. Let cool slightly before serving.