How do you remove the seemingly inherent adding of an enchantment cost to a magical item? Example Steel Armor has a value of 1 on the item menu. I add a reflect magic enchantment to it. When I give it to a vendor it costs 499 gold even though the value is set to 1. I assume is is due to the value of the enchantment. However I see no place to change this. Adjusting the value of the enchantment during it's creation only changes the charge and values of it in and ove itself, not when it is applied to an item. Any thoughts?

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.

To add to that, if you are making a new enchantment in the CS, you can always override the cost of the spell with your own value.