Bring a large pot of salted water to a boil. Add the pasta and cook according to the package directions until barely al dente. Drain and set aside.

While the pasta cooks: In a Dutch oven or similar large, heavy-bottomed pot, heat the butter over medium heat. Once melted, add the onion and cook until the onion is fragrant and beginning to soften but is not yet brown, about 2 minutes. Add the garlic, the sprinkle the flour over the top. With a whisk, stir continually until the flour turns golden brown and the white bits disappear, about 1 minute. The flour will be lumpy at first, but will smooth out as you continue with the recipe.

Pour in the milk a few splashes at a time, whisking constantly to break up any lumps. Bring to a simmer and cook, stirring often, until the sauce thickens, 5 to 7 minutes.

Remove the pot from the heat and stir the salt, pepper and cayenne pepper. Let the mixture cool for 1 minute, then stir in the Greek yogurt and melty cheese. Add the drained pasta and half of the sliced basil. With a large spoon or spatula, stir and fold gently to combine the ingredients and coat each piece of the pasta with the sauce. Taste and add additional salt, pepper or cayenne pepper to taste.

Transfer the mixture to the prepared dish. Sprinkle the parmesan over the top. Arrange the sliced tomato on top, overlapping slightly if needed. Bake on the center rack until hot and bubbly, 15-20 minutes. If you'd like a crispy top, turn the oven to broil and transfer the dish to the upper rack. Broil for 2-3 minutes, until the top if as dark golden and crispy as you like, watching it carefully so that it doesn't burn. Let rest for 5 minutes, the sprinkle on remaining basil and serve hot.

 Refrigerate leftovers in an airtight container for up to 4 days. Reheat individual servings gently in the microwave with a splash of milk to keep them from drying out, stirring periodically.