1 Preheat the oven to 425ºF. Place one rack in the top third of the oven and one rack in the lower third.
2 Prepare the cauliflower and the onions: Trim away the outer leaves and cut the cauliflower into slices roughly 1/4-inch thick. Some smaller florets will fall away; this is fine.
Spread the cauliflower slices and any florets that have fallen off on a rimmed baking sheet. Drizzle with 2 tablespoons of the oil. Using your hands, rub the oil into the cauliflower, coating both sides. Sprinkle with 1/2 teaspoon salt and 1/4 teaspoon pepper.
Roughly chop the onion. On a second baking sheet or in an ovenproof skillet, toss the onions with the remaining 1 tablespoon of the oil and sprinkle with 1/4 teaspoon salt.
(Roasting the cauliflower and onions on separate pans will give them more space and help them roast better.)
3 Roast the cauliflower and onions: Place the cauliflower on the lower rack of the oven and the onions on the top rack. Roast for 25 to 30 minutes, until both are tender and golden. Flip the cauliflower once during roasting; stir the onions occasionally. Remove the onions from the oven if they finish before the cauliflower or start to burn.
Let the vegetables cool slightly in their pans. Break the cauliflower into smaller florets.
4 Lower the oven temperature to 375ºF for baking the pasta.
5 While the vegetables roast, cook the pasta: Bring a large pot of salted water to a boil. Add the pasta to the boiling water and cook for 8 to 10 minutes, or until al dente (do not overcook or the pasta will become mushy after baking). Scoop out and reserve 1 cup of the pasta cooking water.
Drain the pasta in a colander.
6 Assemble the casserole: Return the drained pasta to the pot and immediately stir in 1/2 cup of Parmesan while the pasta is still hot. Once the cheese has melted and absorbed into the pasta a little, stir in the milk.
Add the roasted cauliflower and onion, lemon zest, thyme and Gouda, and stir well. Taste and add more salt and pepper, if you like. If the mixture seems dry, add a little pasta cooking water, a tablespoon at a time.
Transfer to a 3- or 4-quart baking dish.
7 Top with the crispy cracker crumbs: Place the crackers in a zip-top bag and crush with a rolling pin until coarsely crumbled.
In a bowl, mix the crushed crackers with 2 tablespoons Parmesan, the melted butter and parsley. Sprinkle this evenly over the pasta.
8 Bake the pasta: Bake for 35 to 40 minutes, or until the pasta is hot and the top is golden.
9 Cool briefly and serve. Leftovers can be refrigerated for up to 5 days and reheated in a microwave or a warm oven.