I did a bit more research for myself and realized something that makes me look stupid, because I didn't understand the pricing system for awhile.
So if you go back to that Board With Shop Sales On The Wall you can also click each of those sales and find out more details about them. In doing so, I learned how the prices are actually calculated. So each item sold IS getting a profit no matter what because it starts by Adding Together All Of The Parts' Cost (ingots, grips, guards) then adding the Base 10% Mark Up to that amount for a subtotal and then it goes on to adding the Charisma Bonus, which is +1% profit/mark up for every Charisma skill point that is allocated. And finally, there IS a bonus amount of money you gain based on How Fast You Deliver The Weapon.
Heres another screenshot, this one shows the page I'm speaking of and I have underlined each factor for pricing.