Cook the pasta. Bring a large pot of salted water to a rapid boil. Add 1 lb elbow macaroni, then cook according to package directions until al dente, about 5 minutes. Reserve ½ cup of the cooking liquid in a 2-cup measuring cup, then drain the pasta in a colander and set aside.
Dissolve the miso paste. Add 3 Tbsp miso paste to the reserved water, then whisk until dissolved. Set aside.
Optional: add mushrooms. Heat 3 Tbsp butter (reserve the rest) in a large deep skillet over medium-high heat. Add 16 oz (1lb) sliced mushrooms, then cook until browned, stirring occasionally, for 6-8 minutes. Stir in a grated clove of garlic, then cook for 1 minute more.
Make a roux. Stir in 3 Tbsp flour, whisking to combine and cook until absorbed, about 1-2 minutes.
Add the milk. Slowly pour in 3 cups of milk, whisking constantly, until smooth.
Add the cheese. Add 4oz grated white Cheddar, 4oz grated Gruyere, and 4oz grated fontina. Stir until the cheese has melted and the sauce is smooth.
Add the pasta. Pour in cooked elbow pasta, then toss until very well mixed. Remove from the heat, then stir in the miso mixture. Taste and adjust seasoning as needed.
Optional, but recommended. Bake the miso mac and cheese: At this point the mac and cheese can be enjoyed right away. If you’d like it extra cheesy, preheat an oven to 375F, transfer the mac and cheese to a large greased baking dish, then sprinkle with an additional 2-3 oz of grated white Cheddar cheese. Bake for 10-15 minutes, until the cheese on top is melted and bubbly. Otherwise, move onto the next step.
Make the breadcrumb topping. Melt remaining 3 Tbsp of butter in a small skillet over medium-high heat. Add ⅔ cup of panko breadcrumbs, 1 clove of grated garlic, and a pinch of Kosher salt. Cook, stirring occasionally, until toasted and fragrant, about 4-5 minutes. Remove from the heat, then stir in 2 Tbsp grated Parmesan cheese.
Serve! Top the mac and cheese with the breadcrumbs, then garnish with fresh thyme and enjoy!