Combine 1 tablespoon butter and the saffron in a small microwave-safe bowl and microwave until the butter melts, about 1 minute. Let cool 5 minutes. Place the remaining butter and the fennel seeds in a food processor and pulse until smooth. Add the melted saffron butter, 1 teaspoon salt and a few grinds of pepper and continue pulsing until the butter is bright yellow. Transfer to a piece of plastic wrap and form into a 4-inch log; freeze until firm, about 20 minutes. (The saffron butter will keep in the refrigerator for up to 2 weeks.)
Meanwhile, preheat the oven to 425 degrees F. Toss the sliced fennel, garlic, the juice of 1/2 lemon, 1 tablespoon olive oil and 2 tablespoons water in a 9-by-13-inch baking dish. Sprinkle with 2 tablespoons water and season with 1/2 teaspoon salt and a few grinds of pepper. Cover with foil and bake until the fennel is tender, about 20 minutes.
Toss the tomatoes with the remaining 1 tablespoon olive oil and season with salt and pepper. Scatter the tomatoes over the fennel. Set the halibut on top of the vegetables; drizzle with the juice of the remaining 1/2 lemon and season with salt and pepper.
Bake, uncovered, until the halibut is firm and no longer translucent, about 12 minutes; remove from the oven and top each piece with a thin slice of saffron butter. Return the halibut to the oven and bake until the butter just begins to melt, about 2 more minutes. Serve with fennel fronds.