I believe the difference between stock carbon builds pulled out of a mold and serotta or other custom carbon goes beyond fit.
Tubing selection, carbon layup are comparable to ovalizing/butting or varying diameter in tubes--they can produce different ride qualities, and the geometry can be tuned for desired handling characteristics.
The pez review of the Meivici ( http://www.pezcyclingnews.com/?pg=fullstory&id=7853
) offers some insight into the carbon build process at Serotta.
Non custom frames are built to accommodate a variety of individuals of a particular height/inseam. (with a weight range between 120lb flyweights, Clydesdale and beyond) So depending on the rider weight/power output, they may feel drastically different. Moreover, depending on the manufacturer's quality control, the same model have a range stiffness/weight.
Having said all of that, the custom process sort of depends on the knowledge of the customer. If you have a vision of your perfect bike, and an excellent builder, they can help to realize it for you. But for those of us who are unsure if they want to lean or drop into corners, you can either A.) Trust the experience of the builder to produce a nice neutral handling and well fitting frame or B.) find a stock frame that you like and ride it until you discover and can articulate what you like and don't like about it.