Using a sharp knife, very carefully cut the squash in half lengthwise, rocking the knife back and forth. With a spoon, scoop out the seeds and discard. Score the inside of the squash with a criss-cross pattern every inch, brush with 1 tbsp melted butter and season generously with salt and pepper.
Flip the squash upside down (so the inside is facing down) and bake for 30 minutes in a greased casserole dish. Meanwhile, in a small bowl, mix together remaining butter, brown sugar, maple syrup, chili flakes and mustard. After 30 minutes, flip the squash and drizzle the sauce over the squash. Bake another 30 minutes, or until the squash is tender when pierced with a fork.