Make the topping
Combine the flour, brown sugar, granulated sugar, cinnamon, and salt in a medium bowl. Rub in the butter with your fingertips until it's well blended and the mixture is clumpy but still a bit crumbly (it should hold together if you pinch it). Mix in the pecans. Refrigerate until ready to use.
Assemble and bake the crisp
Heat the oven to 375°F. Butter the sides only of a 9-inch-square baking pan.
Peel, quarter, and core the apples. Cut each apple quarter crosswise into 3/4-inch-thick slices. Put them in a large bowl, sprinkle on the cinnamon, and toss until evenly coated. Combine the cranberries and orange zest in a food processor and pulse until the cranberries are finely chopped, scraping down the sides with a rubber spatula as needed.
Add the cranberries to the apples and toss to combine. Put the butter, orange juice, and salt in a small microwaveable dish or a small pan. Heat in the microwave or over medium-low heat until the butter melts, about 1 minute. Swirl to blend and pour the mixture over the apples. Toss to coat. Add the sugar and toss to coat again. Pour the apple mixture into the prepared pan and spread it evenly. Sprinkle the topping evenly on top of the apples.
Line a heavy-duty rimmed baking sheet with foil. Set the pan on the sheet and bake until the juices are bubbling on the sides, the top is golden brown, crisp, and hard, and the apples in the center are tender when pierced with a fork, 60 to 70 minutes (rotate the pan for even browning, if necessary). If the top starts to get too brown after 45 minutes, cover it loosely with aluminum foil. Let cool on a rack for at least 30 minutes to let the juices thicken. Serve warm.