Let me elaborate. I have three bikes. One is a Bridgestone XO-2 I bought off Craigslist. I wanted one for years and was fortunate to find one in my size. The only way I'd get a bike with that geometry and 559 wheels new would be to go custom.
My other two bikes(a Gunnar Sport and a Surly Pacer) are semi-custom. By that, I mean I bought the frame and fork from the LBS and had them build with components of my choice. The Gunnar got way expensive that way, but the price of the Surly build was competitive with the other bikes on the LBS's floor.
It seems that the majority of posters, when they buy new, buy a complete bike from one of the big makers. Did your LBS mention the option of building up a bike from the frameset?