Combine broth, water, parsnips, garlic, bay leaf, thyme, salt, and pepper in a large pot and bring to a boil. Reduce heat to a simmer, cover partially, and cook until parsnips are tender, 15 to 20 minutes. Drain and transfer to a large bowl.

Preheat the oven to 375 degrees F (190 degrees C). Coat a 9-inch glass pie plate with 1 tablespoon butter.

Add 1/2 cup butter, nutmeg, and lemon rind to the bowl with the parsnips. Use an electric mixer to beat until mixed thoroughly but still slightly chunky. Transfer mixture to the prepared pie plate.

Melt remaining butter in a large, heavy skillet over medium-high heat. Add onion and saute until translucent and beginning to brown, about 10 minutes. Spread onion evenly over parsnip mixture.

Place apple slices in a bowl and add a squeeze of lemon juice; toss to coat. Spread apple slices evenly over onion. Season with additional lemon juice, nutmeg, and pepper.

Bake in the preheated oven until heated through and top is beginning to crisp, about 25 minutes.