This holiday side is as flavorful as it is colorful.
Arrange the rack in the middle of the oven; preheat to 325°.
On a large rimmed baking sheet, toss the pepitas with 1/2 tsp. oil. Bake for 5 minutes. Toss the pecans with the pepitas. Bake until fragrant, 8 to 10 minutes more. Immediately transfer to a bowl and toss with the za’atar, cayenne, and 3/4 tsp. salt; let cool.
Increase the oven temperature to 450°.
On a large rimmed baking sheet, toss the squash with 1/4 cup oil; season with salt and pepper. Spread in an even layer on the baking sheet. Roast until tender and golden, 40 to 45 minutes.
In a small pan, bring the vinegar, sugar, 3/4 tsp. salt, and 1/4 tsp. pepper just to a boil over medium-high heat, whisking to dissolve the sugar. Add the red onions, return to a boil, then remove from the heat. Let cool to room temperature, about 20 minutes.
Transfer the squash to a platter. Top with half of the pickled onions. Coarsely chop together the pecans and pepitas. Adjust the seasoning, then sprinkle 1/ 3 cup of the dukkah over the squash. Top with the parsley. Serve the remaining onions and dukkah on the side.