Preheat the oven to 350 F. Cook the pasta according to the package instructions — just under al dente.
In a small bowl, mix the panko with 2 tablespoons melted butter, and a pinch of salt until moist. Set aside.
In a large saucepan or deep skillet over medium heat, melt the remaining 4 tablespoons of butter. Whisk in the flour, and mix constantly until smooth and golden.
Whisking constantly, add the milk 1 cup at a time, incorporating into the roux until smooth. Allow to thicken slightly, about 3 minutes.
Add the mozzarella, and stir until smooth. Add the cheddar, and stir until combined. Add the fontina, and allow to melt into the sauce, stirring frequently to avoid burning. If the sauce becomes too thick, add more milk.
Stir in the thyme, garlic powder, salt, and pepper to taste. Add the cooked macaroni, and combine until noodles are coated.
Pour the mixture into a casserole dish. Sprinkle the panko blend generously on top, then add thyme sprigs. Place in the oven, and bake until panko is golden brown, about 30 minutes. Remove from the oven, and serve immediately.