Cut the squash in half lengthwise and scoop out and reserve the seeds in a small bowl. Cut the squash into 1-inch half-moons and place into a large bowl.
Thinly slice 1 of the jalapenos and place in a small bowl with the white balsamic, making sure the vinegar covers the peppers completely. Set aside to pickle while the squash cooks.
Meanwhile, thinly slice the remaining jalapeno and transfer to a small skillet with 1/4 cup of the olive oil and 1 teaspoon of the harissa. Cook over medium-high heat, stirring frequently, until the peppers are shimmering and starting to lighten in color in the center and the seeds are turning golden brown, about 5 minutes. Strain the oil into the large bowl with the squash and add the remaining 2 teaspoons harissa, 1 teaspoon salt and a generous amount of freshly ground black pepper. Use tongs (the oil will be hot) to toss everything together. Transfer to a baking sheet and bake until a butter knife can be inserted easily into the squash and removed, about 30 minutes.
While the squash is cooking, toss the seeds with the pumpkin pie spice, cayenne pepper, remaining 1/2 teaspoon olive oil, 1/4 teaspoon salt and a few grinds of black pepper. Transfer to a baking sheet and bake until light golden and crispy, 7 to 8 minutes.
Transfer the squash to a serving platter. Drain the jalapenos and sprinkle over top along with the feta cheese and roasted seeds.