Cook pasta in a large pot of salted water according to package directions until a few minutes shy of al dente. Drain.
Meanwhile, in a medium bowl, combine the melted butter and crackers and mix until well blended.
Heat oven to 375 degrees. In a large Dutch oven, melt the remaining 4 tablespoons butter over medium. Add flour and cook, whisking frequently, until well incorporated and flour is no longer raw, about 1 minute. While whisking constantly, add milk in a slow, steady stream. Add miso, season with salt and pepper and bring back to a simmer, whisking occasionally and mashing the miso to help it dissolve. Cook, whisking frequently, until mixture is smooth and slightly thickened, 3 minutes.
Turn off heat and add mustard, Cheddar, Gruyère and Parmesan. Whisk until smooth and season with salt and pepper.
Add pasta to the cheese sauce and mix well. Stir scallions into the cracker mixture, then scatter it over the top of the pasta in an even layer. Bake until golden brown, 20 minutes.
Serve warm in shallow bowls. Garnish with more scallions and pepper, if desired.
