Step 1Heat the oven to 375 degrees. Cut the squash in half, slicing through the stem end. Scrape out the seeds (a melon baller or grapefruit spoon makes it easier). Cut the squash halves crosswise in half. Lay each quarter cut-side down on a cutting board and, using a vegetable peeler or very sharp paring knife, cut away the skin. Cut the squash into roughly three-fourths-inch chunks and place in a large bowl.
Step 2Add the thyme, pepper flakes and salt and toss to mix. Pour the oil over and mix thoroughly with a rubber spatula until all the chunks are evenly seasoned and oiled. Place the squash in a single layer on a rimmed baking sheet.
Step 3Roast, stirring once, until all the squash chunks are tender and caramelized on the bottom, 15 to 20 minutes. Serve hot or warm. (This can be made ahead and reheated in the oven, uncovered.)