Interesting....the "assembly charge" on the two bikes I had built this winter were both under $100. But, I would guess that I paid more, relatively speaking, for the parts. It is all marketing. But good marketing--with those prices I'd only build myself if I wanted the experience.

So, if you want the experience building a bike, do it, but, as others have said, work with the LBS for the parts so that they work together. This winter I built up two bikes, a purrrrr-ty Waterford with Campy Chorus and a Surly Pacer, dubbed Slush Kicker, for riding in sloppy weather.

Needless to say the Pacer did not get high-end components and, given that here in the snow-bound north, roads are either white with snow cover or white with salt crust, I really didn't want to spend much on Pacer parts that would need replacement every few years or so.

The LBS was great....he pulled out sale catalogs and closeouts and successfully built up a bike that would have cost 1.5 times what I paid for it if it was "off-the-shelf". Very unusual, since the big manufacturers pay a fraction of what we do for the components--as you discovered when you costed out the Big Dummy. For the Pacer build the LBS was invaluable--they have connections.