Put a pizza stone on a rack in the upper third of the oven. Preheat the oven to 550 degrees F and let the stone heat at that temperature for 10 minutes.
Stir the creme fraiche, nutmeg and egg yolk together in a small bowl with a large pinch of salt and a few grinds of pepper.
Put the bacon in a large skillet over medium heat and cook, stirring occasionally, until some of the fat has rendered and the bacon is just starting to crisp, about 7 minutes. Carefully drain off most of the fat, then add the leeks. Cook, stirring, until the leeks just start to wilt, about 3 minutes.
Divide the pizza dough in half and lay on a lightly floured work surface. Roll and stretch one piece of dough into a very thin, organic shape (1/8 to 1/4 inch thick). Put the dough on a piece of parchment paper. Spread half of the creme fraiche mixture evenly on top, leaving a 1-inch border all around. Top with half of the bacon and leeks, then top with half the Gruyere. Put the pizza and parchment on a flat baking sheet or pizza peel and transfer to the pizza stone; bake until the crust is golden brown and charred in spots, 8 to 10 minutes. Repeat with the remaining dough and toppings. Cut into pieces and serve warm or at room temperature.