Preheat the oven to 400 degrees F and line 2 baking sheets with foil. Whisk the melted butter, orange juice, sugar and vinegar in a large bowl. Add the squash, chiles, garlic, thyme, 1 teaspoon salt and a few grinds of pepper; toss to coat.
Divide the squash mixture and liquid between the prepared baking sheets, spreading the squash in a single layer. Sprinkle with the sesame seeds. Roast, flipping the squash halfway through, until the squash is tender and caramelized in spots and the sesame seeds are lightly toasted, about 40 minutes. (The squash can be made up to 4 hours ahead. Serve at room temperature.)