In a medium saucepan, bring the broth and 2 1/2 cups water to a low simmer; cover.
Grease a 9-inch square baking dish. In a saucepan, melt 2 tbsp. butter over medium heat. Add the shallot and cook until softened, 3 minutes Stir in the rice and 1/2 cup of the broth mixture, stirring constantly until the liquid is mostly absorbed. Continue adding the broth in 1/2-cup increments, stirring until nearly absorbed before adding more, and adjusting the heat to maintain a simmer, for about 20 minutes total. Stir in the lemon zest and 1 tsp. thyme. If the rice is still firm, stir in more broth and cook longer.
Remove the pan from the heat and stir in 2 tbsp. butter, 1/2 cup cheese and the peas; season with salt and pepper. Spread the mixture evenly into the prepared baking dish, then refrigerate until cold (up to 1 day).
Preheat the oven to 375 degrees . In a medium saucepan, melt the remaining 4 tbsp. butter over medium-low heat. Whisk in the flour for 2 minutes. Whisk in half of the milk until smooth, then gradually whisk in the rest to make a thick sauce; cook, stirring, for 1 minutes. Whisk in half of the squash puree and remove from the heat.
Whisk the egg yolks into the remaining squash puree, then stir into the sauce with the remaining 1 tsp. thyme, 2 cups cheese and 1/4 tsp. each salt and pepper.
Using an electric mixer, beat the egg whites with a pinch of salt just until soft peaks form. Gently fold the whites into the squash mixture until no white streaks remain; spread evenly onto the cold risotto. Bake until the top is golden-brown and the souffle is cooked through, 45 minutes. Let sit loosely covered with foil for 15 minutes before serving.