Yes, you can certainly peel the butternut before the initial roasting. If you do this I would estimate that the cooking time should be reduced to about 25 minutes. However, if you do roast the butternut without the skin you should take care not to overcook it or you will find it difficult to turn the butternut to stuff it. You can also peel the butternut after it has been roasted, but once again, depending on how soft the butternut is, it may be difficult to turn over and stuff. It's much easier to leave the skin on, stuff the butternut and let everyone remove the skin onto a plate at the table.