I have small and large fiber neuropathy, with the muscle wastage you describe and I would say the sharp, shooting pains, which are the worst and the main reason I am on pain meds, feel like they are coming from the long bones in my legs. It is such a deep, serious pain and I really couldn't function with it.
I spent years before it got unbearable thinking I just had bad varicose veins or something since I had restless legs all my life and leg pain. Hereditary neuropathy pretty much explained all the symptoms I was having.
With the way all the nerves get messed up the signals just feel like they are coming from the bones. It is the best way to describe the pain, but isn't necessarily the reality. I think the pain comes from the nerves themselves, although some of it may be from trying to function with weakened muscles. I think the overwhelming fatigue I have is from this,