Combine scallops, shrimp, salt-free Cajun seasoning, garlic powder, smoked paprika, cayenne, and Kosher salt in a bowl, tossing until every piece is evenly coated.
Warm a skillet over medium-high heat, swirl in the olive oil, then sear the seafood until browned and opaque—about 1 ½–2 minutes per side—before transferring it to a plate.
Bring a generously salted pot of water to a rolling boil, cook the cavatappi to al dente according to the package, drain, and, if the sauce is not yet ready, lightly oil the pasta to prevent sticking.
While the pasta cooks, heat the whole milk and half-and-half until steaming but not boiling.
In a heavy saucepan melt the butter over medium heat, whisk in the flour, and cook—whisking constantly—until the roux turns light caramel, roughly 3–4 minutes; reduce the heat.
Gradually pour in the hot milk mixture while whisking; the sauce will loosen as all the liquid is incorporated.
Return the heat to medium, whisk until the béchamel thickens enough to coat a spoon (3–5 minutes), then lower the flame.
Season the sauce with Kosher salt, Cajun seasoning, cayenne, and smoked paprika, adjusting to taste.
Stir in all the Monterey Jack, plus ½ cup each of cheddar and Pecorino, until fully melted; if it thickens excessively, temper with a splash of warm milk.
Fold the cheese sauce and sautéed seafood into the pasta, holding back about 1 cup of noodles to fine-tune the consistency; add the reserved pasta only if the mixture feels overly loose.
Transfer the mac and cheese to a deep-dish pie plate or 9 × 9 in casserole, scatter the remaining cheddar and Pecorino over the top, and broil 4–5 minutes until the surface blisters to a golden finish. Serve immediately.