Heat a smoker to 225°F using a mild cooking wood such as apple. Cook macaroni in a large pot of water with the tablespoon salt until 2 minutes short of the package time; drain.
While the pasta cooks, melt butter in a saucepan and whisk in flour for 1 minute. Gradually add milk, then mustard, sauce salt and pepper; simmer for 4 minutes.
Remove from the heat and stir in cheddar, Monterey Jack and cream cheese until smooth. Fold in the macaroni and transfer to a shallow 9-by-13-inch metal pan.
Smoke uncovered for 60 to 75 minutes, stirring gently once after 30 minutes, until the sauce is bubbling, the surface has light color and the center reaches 165°F.
Rest for 5 minutes before serving, keeping the creamy center under the lightly smoked surface.