According to the wiki it comes from the "Constant Effect Barter Factor" defined for the Magic effect that underlies the enchantment (for armor/clothing where the effect is constant). I would assume if you set it to zero, then the price of enchanted and unenchanted would come out the same. Of course, changing it for reflect magic would do the same to every item that reflects magic, so you might have to do some effect cloning.
For a weapon, the amount of charge held affects the price.