Preheat oven to 425°F with rack in upper third. Lightly butter a 2-to 2 1/2-quart shallow baking dish.
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.
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 Gruyère, nutmeg, and 3/4 teaspoon salt. Cover and set aside, whisking occasionally.
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.
Spread 1/2 cup cheese sauce in bottom of baking dish.
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 Gruyère and bake until top is just bubbling and slightly browned, 15 to 20 minutes.
Let stand 5 minutes before serving.
—Lasagne can be assembled 1 day ahead and chilled.
Let stand at room temperature 30 minutes before baking.—Any leftover polenta log can be sliced and sautéed in oil or butter to serve with eggs at breakfast.
