Place a rack in the center of the oven and heat it to 425°F (220°C). Line a large rimmed sheet pan with parchment paper.
Trim both ends of the squash, peel it, cut the neck from the round bottom, halve the bottom and scoop out the seeds. Cut everything into even 1-inch cubes.
Toss the cubes on the sheet pan with the olive oil, salt and pepper. Spread them in a single layer with a little space between pieces.
Roast for 20 minutes, until the undersides are starting to brown.
Meanwhile, stir together the honey, melted butter, cinnamon and cayenne. Drizzle it over the squash and toss gently with a spatula, turning the cubes over.
Roast for 10 to 15 minutes more, until the cubes are fork-tender and the edges are caramelized. Watch the last few minutes closely, since honey darkens quickly.
Let the squash rest on the pan for 2 to 3 minutes so the glaze sets, then sprinkle with thyme and flaky salt and serve warm.