Preheat the oven to 180 degrees C, and roast the squash with olive oil till lightly browned and cooked. Cool while making the muffin batter.
In a large bowl, mix the flours, baking powder, salt, pepper and chilli flakes. Then mix in the vegetables (reserving some squash for topping the muffins), peeled and smashed garlic, bacon and feta.
Beat the milk and eggs together in another bowl before adding to the dry mixture. Check the seasoning, heap into greased muffin molds,and top with the remaining roasted squash. Bake for 20-25 minutes or till a toothpick inserted into them comes out clean.