Jeff –
A lot of the parts of a PowerMac are the same commodity parts as a high-end Windows PC: lots of fast RAM, a big hard drive, a sexy video card. Apple doesn’t see the volume for their PPC chips and motherboards that other manufacturers might, but they probably do better business for their motherboards than some of the smaller x86 motherboard makers.
I think that you are right about the economies of scale benefitting Windows PC makers though. I suspect that the real reason for Apple’s high prices are a combination of less volume, less competition and some factors we haven’t thought of.