As Ben noted in an answer, "the body doesn't spend the whole night coming into thermal equilibrium with its surroundings." Where the body needs to focus its energy is important because if your body is busy heating your core to avoid death, then your fingers and toes can't get as much warming attention and will be more likely to go numb and eventually become frostbitten. Thus, keeping a comfortable core temperature without expending extra internal energy to do so will help keep your fingers and toes a little warmer. (Consider how a proper jacket can help your overall comfort in cold weather, especially if you get blood flowing in your hands and feet. That warming blood flow lasts longer in my extremities if my core is well insulated than if my core is rapidly losing warmth.

Related to that, I always think of the need to relieve yourself before bed at camp as related to muscles and energy expenditure with them. If you need to pee and are holding it in whether consciously or not, muscles are working to do that. The blood and energy going to the muscles that are keeping you from wetting your sleeping bag, could be going to your fingers and toes.

That said, the real scientific answer is in biology, and is beyond the outdoor experiences I've had and been advised by.