I own two completely custom bikes and two bikes built up from stock frames. The custom frames not only fit perfectly but they provide the ride I specified that I wanted them to have when I ordered them. There are little "extras" built into the frame (S&S couplings, fender mounts, removable dropouts). All four bikes have the components that I specified (right down to the spoke nipples) which can also be of importance.
The custom frames are both Seven frames and the fitting took two hours.