I think you're misunderstanding custom bike prices. Yes, if
you bought the parts it would possibly cost more than buying an off-the -peg full bike, but the companies that specifically build custom bikes get these parts at trade prices, so they are buying them cheaper than you could. Yes, they stick their profit margins on top, but they often have less overheads than the bigger chains and can often put together a better specced bike for a price as good, if not better than a standard offering from the usual bike stores.
I'm not saying that's always the case, but it's worth a look.
Just as an example take a look here:
http://www.kinetic-one.co.uk/