Cook pasta in a large pot of boiling salted water (open flame broiler). Cook to al dente (6-8 mins). Strain and rinse with cool water, set aside.
Melt 2 Tbsp butter in skillet and add panko. Stir until bread crumbs have browned, transfer to a small bowl and add the parmesan, thyme leaves, and ¼ tsp salt.
Bring milk to a bare simmer in small saucepan — keep warm.
Melt 2 Tbsp butter in medium saucepan. Add onion and garlic. Stir until onions begin to soften and are fragrant. Sprinkle flour over them and continue cooking, stirring constantly.
Once the mixture begins to stick to the bottom of the saucepan (about 1 min), start slowly adding in the warmed milk. Whisk to combine after each addition.
Bring sauce to a boil once combined, then reduce the heat to a simmer. Stir until the sauce has thickened and doesn't feel/look grainy (6-8 minutes).
Add fontina, cheddar, Gruyere, cayenne and red pepper flakes (to taste), mustard powder, and 1/2 tsp salt.
Remove from heat and mix in pasta.
Transfer mixture to a 2-quart baking dish.
Top with panko, parmesan mixture.
Bake 8-10 minutes — until sauce is bubbling around the edges. Let cool in pan for 15 minutes before serving.