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1
Preheat oven to 425u00b0F with rack in upper third. Lightly butter a 2-to 2 1/2-quart shallow baking dish.
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2
Melt butter in a 2-to 3-quart heavy saucepan over medium heat. Whisk in flour until smooth, then cook roux, whisking frequently, until pale golden, 2 to 3 minutes.
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3
Meanwhile, heat milk in a separate small saucepan until just about to boil. Add milk to roux in 2 batches, whisking constantly until very smooth. Bring to a boil, whisking, then cook, whisking, 30 seconds. Remove from heat and whisk in Fontina, half of Gruyere, nutmeg, and 3/4 teaspoon salt. Cover and set aside, whisking occasionally.
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4
Cook garlic in oil in a 12-inch heavy skillet over medium-high heat, stirring, until beginning to turn pale golden. Stir in mushrooms, 1/2 teaspoon salt, and 1/4 teaspoon pepper and cook, stirring occasionally, until mushrooms are softened, about 3 minutes. Add seitan and thyme and cook, stirring occasionally, until mushrooms and seitan are slightly golden, about 4 minutes. Add water and cook briefly, scraping up any brown bits.
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5
Spread 1/2 cup cheese sauce in bottom of baking dish.
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6
Slice 1 log of polenta into 1/4-inch-thick rounds and arrange enough rounds to cover bottom of dish, overlapping slightly. Spoon half of filling evenly over polenta, then spread with half of remaining cheese sauce (about 1 cup). Slice enough rounds from second log to form a second layer. Cover with remaining filling, then cheese sauce. Sprinkle with remaining Gruyere and bake until top is just bubbling and slightly browned, 15 to 20 minutes. Let stand 5 minutes before serving.
