If your supply is significantly constrained there is little sense in marketing something at the going rate because you would be sold out constantly. Thus you raise the price to moderate demand until constraints can be dealt with. Frankly the electronics. Industry has operated this way for years and is one reason why Intel can charge a premium for their processors. Intel is almost two nodes ahead of the rest of the industry and can take that advantage and charge higher prices as the roll out new chips.
So maybe it is best to say the retina MBPs are over priced due to constrained supplies.
The prices are great for Apple as long as they can continue to charge those prices. But as supply catches up with demand and the competition starts to make use of those screens Apple will have to moderate prices. In the end the retina machines shouldn't cost anymore than the standard screened machines.
But none of that is being overpriced if you are selling as many as you can make. You have to assume Apple is pretty good at estimating how many units they can make and how many they can sell. Based on how quickly and how long they are backlogged there is an argument for their products being underpriced.
I have no idea how you've come to a conclusion that Retina displays shouldn't cost anymore than the previous displays. We're talking 4x as many pixels in the same display area. With the iPod Touch and Mac notebooks we're also talking about going from TN to IPS panels. How would these not cost more? Eventually the cost will come down but you have make and sell enough of them for that to happen.
Frankly, I think the cost of the Retina MBPs are amazingly low. Apple seems very aggressive to make them look more attractive than the previous style MBPs they did a spec bump on.