Bring a few inches of water to a boil. Salt water and parboil broccoli, rabe or broccolini 4-5 minutes. Drain and cold shock, then dry on kitchen towels.
Bring a large pot of water to a boil for the pasta and undercook the pasta by about 2 minutes. Preheat oven to 425°F.
Heat a saucepot over medium heat with EVOO and butter. Sauté shallots, garlic and chilies 2-3 minutes then add flour and stir 1 minute. Whisk in milk and season sauce with salt and pepper, melt in cheddar and Gouda.
Combine pasta with broccoli, broccolini or rabe and the sauce, and transfer to a baking dish. Top with Parm cheese, sprinkle with fresh thyme and bake until brown and bubbly.