In a large ovenproof skillet or fireproof casserole set over medium heat, melt the butter. Add the leeks, broccolini stalks, garlic and thyme and cook, stirring frequently, until the vegetables are softened, about 15 minutes. Stir in the flour, then slowly stir in the milk. Cook, stirring frequently, until slightly thickened, 5 to 10 minutes.
Add the macaroni to the boiling water and cook for a minute or two less than the package instructions, until al dente. Drain.
While the pasta is cooking, stir the Parmesan and all but a few tablespoons of the Cheddar into the sauce and mix well. Transfer to a blender (or use a handheld immersion blender), add the spinach and purée until smooth. (You may need to work in batches to avoid overcrowding the blender.) Stir in the 1/2 teaspoon salt and pepper, taste, and add more, if needed.
Return the sauce to the skillet or casserole and stir in the pasta and broccolini florets, loosening with a splash of milk, if needed. Sprinkle the remaining Cheddar on top, along with the almonds.
Transfer to the oven and bake for about 30 minutes, or until golden and bubbling. Serve hot.
Nutrition information per serving: