Grease a 9-by-13-inch casserole dish with coconut oil. If baking immediately, preheat the oven to 325°F. Leave the oven off for the make-ahead freezer route.
Place the cooked butternut squash, homemade coconut milk, eggs, raw honey, melted and cooled coconut oil, homemade vanilla, sea salt and cinnamon in a large food processor. Puree 30 to 50 seconds, stopping once with the machine off to scrape the sides and base, until uniformly smooth with no squash pieces or egg streaks. Work in two evenly divided batches if needed.
Spread the puree evenly in the prepared casserole dish, reaching the corners and leaving the surface smooth.
Clean and dry the processor. Process the properly prepared, fully dried pecans into a coarse meal with visible tiny nut pieces. Stop before the meal becomes glossy or pasty.
Add the homemade coconut flour, egg yolks, raw honey, room-temperature coconut oil, cinnamon and sea salt. Pulse just until moist irregular clumps form. Scatter the raw crumb evenly over the squash filling, including the corners.
For immediate baking, bake at 325°F for about 60 minutes. Begin checking at 45 minutes and cover loosely if the crumb browns too quickly. The casserole is ready when the topping is golden rather than dark and the hot center has only a slight jiggle.
For make-ahead preparation, cover and freeze the assembled unbaked casserole. About 24 hours before serving, move it to the refrigerator and uncover it while it thaws. Once thawed, bake at 325°F using the same golden-topping and hot, slightly jiggly-center cues.
Rest the baked casserole for 20 minutes before serving so the soft center can settle further.