They can pretty much charge what they want really. Some places are just more expensive than others, as they mark their items up more than their competitors for various reasons. That is why it is wise to shop around before settling on a particular shop to work on your car. Find one with good/reputable service, reasonable prices and one that you can trust and stick with it. The place I go to for my car is a little on the pricey side, but the service is exceptional and I can trust these folks. I had a part stolen right off my car at one place, so I try to be careful when it comes to my car and I won't just take it anywhere, even if it is cheaper. You get what you pay for.
I have owned and operated a couple of shops and currently operate a parts store. Most shops will generally mark up parts 30%. Considering that at the parts store level they don't have much mark up at the retail level they can not deliver a part to a shop much cheaper than retail. The shop must also pay the mechanic and operating costs (lights, specialty tools ,diagnostic equipment. Haz mat disposal, training, etc.) so generally the price the shop charges you will be higher than retail. Keep in mind he still has to pay the cost to run his business so if he allows you to supply your own parts than he will generally charge a higher labor rate. Supplying your own parts will also affect any warranty's he may offer (parts stores do not reimburse labor at a retail level on warranty claims). People often assume they are getting the screws put to them by mechanics because they do not understand all it takes to repair their vehicle . To put it in perspective try this. Go to your grocery store and pick up a bag of hamburger buns and a pound of hamburger then take it to your local McDonald's and see what they charge to make you four burgers.
No, they should be charging you the retail price, this is one of the two ways they have to make any money. One way is the labor charge, which pays the mechanic and part of the overhead (operating expenses). The other way is by marking up the price on parts, this hopefully pays the rest of the overhead, and leaves a little left over for the shop owner. Any shop owner who charges wholesale for parts is going to starve, unless he can find some other way to get money out of you (maybe cheat).
Thanks for that extra insight into the Parts Business sinned. OK on the 30% markup too. It seems the shop is way above that unless they are getting gold plated Blower motors or something. I would not actually be buying a part at a lower price and bringing it in -- just use the info to ask questions about why their price is so much higher (and I don't even know if they are using Genuine Ford Parts even).
The garage pays the wholesale price. They then add a markup and sell the part to you at the retail price.