Preheat the oven to 400°F (205°C) and place a rack in the middle position.

Bring a large pot of salted water to a boil. Add the cauliflower florets and cook 5 minutes — they should be very al dente. Drain thoroughly and transfer to a colander or clean towel to let excess moisture drain; set aside.

Warm the 2 cups whole milk until hot to the touch but not boiling (microwave briefly or heat gently in a small saucepan).

Make the sauce: Melt the 3 tablespoons unsalted butter in a medium saucepan over medium heat. Whisk in the 1/4 cup all-purpose flour and cook 1 to 2 minutes, stirring, until bubbling but not browned.

Gradually whisk in the warm milk until smooth. Bring the mixture to a gentle boil, whisking often and scraping the pan edges to prevent lumps. Reduce the heat and simmer, whisking frequently, until the sauce thickens and coats the back of a spoon, about 3 to 5 minutes.

Remove the saucepan from the heat and stir in salt and freshly ground black pepper to taste, a pinch of ground nutmeg, 1/2 cup shredded Gruyère, and 2 tablespoons grated Pecorino Romano or Parmigiano Reggiano. Whisk until smooth.

Spoon about one-third of the sauce into the bottom of a 2-qt (or 8-inch/20-cm) square baking dish and spread to cover. Arrange the par-cooked cauliflower evenly over the sauce, then spoon the remaining sauce over the florets so they are well coated. Sprinkle the top with the remaining 1/2 cup shredded Gruyère.

In a small bowl, toss the 1/2 cup panko breadcrumbs with the 1 tablespoon extra-virgin olive oil, the remaining 2 tablespoons grated Pecorino Romano or Parmigiano Reggiano, the 2 teaspoons fresh thyme (or 3/4 teaspoon dried), and salt and freshly ground black pepper to taste. Sprinkle this breadcrumb mixture evenly over the cauliflower.

Bake uncovered for 25 to 30 minutes, until the topping is golden brown and the sauce is bubbling around the edges. Let the gratin rest at least 10 minutes before serving to allow the sauce to set.