Set the oven to 425°F / 220°C, or 200°C fan, and prepare two baking trays with a light coating of grease beneath parchment paper. The parchment should lie flat so the dough portions sit evenly.
Heat the water, cubed butter, and measured salt in a saucepan over medium-high heat until boiling. Check that no solid butter remains before adding the flour.
Take the pan off the heat and beat in the flour, nutmeg, and black pepper. Keep mixing until the dry flour disappears into a cohesive paste.
Cook the paste over low heat for 1 minute, stirring and pressing it around the pan. A thin pale film on the bottom and dough gathering away from the sides indicate moisture is evaporating.
Move the saucepan off the burner and let the paste cool for 2 minutes. It should remain warm but no longer be bubbling hot when the eggs go in.
Beat the first egg thoroughly into the warm paste with a wooden spoon or electric beater. The mixture may look slippery and broken before it becomes cohesive again.
Work in the remaining three eggs individually, fully blending each one before continuing. The finished dough should look glossy and fall slowly from the spoon in a thick ribbon.
Fold the 2 cups of freshly shredded Gruyère into the dough. The cheese should spread evenly through the mixture rather than collect in clumps.
Portion tablespoon-sized mounds onto the prepared trays using a small cookie scoop or two spoons, leaving room for expansion. Aim for matching sizes so the puffs brown at a similar rate.
Apply a light coating of egg yolk with a pastry brush and distribute the reserved topping cheese over the mounds. Keep the topping on the dough rather than scattered across the parchment, where it can burn.
Bake for 25 minutes, keeping the oven door closed during the first 20 minutes. Look for puffed, golden shells and a nutty toasted-cheese aroma rather than pale, soft-looking surfaces.
Let the baked puffs cool for 15 minutes before serving warm. This pause allows the exterior to become crisper as steam escapes from the centers.