Preheat oven to 375F. Line a 6-cup standard size muffin pan with easy release liners and set aside. You can also use 6 silicone cupcake molds.
Bring a pot of water to a boil. Cook macaroni according to package directions. Drain and cover to keep warm.
Heat butter and flour in a large pot set over medium-high heat. Once flour starts to bubble add milk and whisk until a thick sauce forms.
Pour macaroni into the sauce and toss until evenly coated. Stir in mozzarella and habanero jack until the cheese has melted. Remove from the heat.
Sprinkle cotija cheese on bottom of each cupcake liner. Fill with macaroni about 3/4 full.
In a small bowl combine jalapeño and breadcrumbs. Sprinkle over macaroni cups. Nestle half a cherry tomato in the center of each cup, cut side up.
Spray tops of macaroni bites with cooking spray and transfer to oven. Bake until breadcrumbs are golden and cheese bubbles, about 15 minutes.