Sigh...
The article I cited was to give you a general background, which is what wikipedia is good for. What it isn't good for is claiming truth from it, as we all know.
Phantom limb is interpreted in many ways. For instance, I can argue against wikipedia and say that because the end neurons are sending a message to the brain, which is the cause of the sensation of phantom limb.
Before you respond, realize that the motor cortex is not the command center, it is just reflective to the peripheral nervous system. Shown here:
http://upload.wikimedia.org/wikipedia/en/1/13/Sensory_Homunculus.png
When electrically probed in the corresponding areas, you will feel a sensation in that area. A probe in the pinky would cause a reaction in the brain in the corresponding area. So which way is it? The pinky giving the command "Hey I feel something!" or is the brain saying that?
This type of thinking isn't my own random thoughts. It's what contemporary psychologists have been struggling with in recent years. The old ideology that the brain is the "command center" is outdated, as is Freud and Skinner. Theories get replaced by more accurate ones. It's just science.