Summer Squash Gratin With Pickled Rye Bread Crumbs

2 pounds medium zucchini, yellow summer squash or a combination, trimmed
Kosher salt
6 tablespoons unsalted butter (3/4 stick)
3 cups rye bread crumbs (about 8 ounces), preferably from day-old seeded or seedless loaf
3 tablespoons pickle juice, from a jar of dill pickles
1 large yellow onion, halved and thinly sliced
1 tablespoon minced garlic (about 2 large cloves)
1 teaspoon roughly chopped fresh thyme leaves
¼ teaspoon red-pepper flakes
½ teaspoon black pepper
1 ½ cups grated Gruyère (about 4 ounces)

Heat the oven to 400 degrees. Slice squash 1/4-inch thick, sprinkle with 2 teaspoons salt, and place in a colander set in the sink for at least 30 minutes and up to 1 hour, tossing occasionally with your hands. Gather the squash in a kitchen towel or paper towel and squeeze gently to remove excess moisture.
While the squash drains, melt 3 tablespoons butter in a 10-inch cast-iron skillet over medium heat. Add the breadcrumbs, 1 tablespoon pickle juice and 3/4 teaspoon salt. Stir until all the butter is absorbed, transfer to a bowl and set aside. Wipe the skillet clean using a paper towel.
Heat 1 tablespoon butter in the skillet over medium-low. Add the onions and cook, tossing occasionally, until the onions are lightly caramelized, 15 to 20 minutes. Add the remaining 2 tablespoons pickle juice, the garlic, thyme, red-pepper flakes, pepper and 1/2 teaspoon salt and cook until the garlic is fragrant, about 1 minute. Off the heat, stir in 2 tablespoons butter until melted.
Add half the squash to the skillet and toss with tongs until combined. Add the rest of the squash and toss again. Add the Gruyère, along with 1/3 of the bread crumbs and toss well. Arrange into one packed layer, sprinkle with the remaining bread crumbs and bake until browned and bubbling, 30 to 35 minutes. Serve hot.