The car yards have to pay staff, council rates, water, electricity, building maintainence, insurance etc among a host of other costs. How do they do that?
They do it by buying product low and then selling product high, that's how a business works like Real estate, supermarkets, even your local pub etc. Does anyone think that pubs pay the breweries $2.50 a pot or whatever the going price over the bar is thesedays? Of course not because they have to make a profit. What they buy the product for and what every business sells it for are two different things.
Because most of us are just consumers we tend to think that we are getting ripped off. They are in the business of selling cars and they only think about what they can get for it plus overheads. Lowered suspension and engine mods don't mean much to the person who will buy the car from their yard down the track so they aren't going to pay extra for those in the tradein.
For example if you buy a meatpie at a hotfood shop you will pay more then if you bought a box of them at the supermarket and took them home to heat up yourself.
Going to a caryard just happens to be a faster and more convenient way to shop for and buy a car but you have to pay a premium for that kind of service.
Auctions and private sales are the way to go for getting the best deals.
Same thing if you want to buy a Playstation2, check out the trading post and compare the difference in price between a new one from Kmart and a secondhand one.