I understand the position that any body assembled on a frame/jig that is "to specs" should fit any other frame that is also "to specs", but the specifications have manfacturing tolerances. While they will be close I would challenge that no two frames are going to be truly identical, hence the need for shims to get the gaps right. This is the benefit of having your body assembled on the frame it will ride on - tolerances are accounted for in the body assembly.
From the August '08 build article in Street Rod Builder, N&N not only mounts the floor with the body on the frame, they also build the doors up from inner & outer panels clamped in place on the body to make initial gaps right. They offer a complete chassis/body combo as Mike points out, but I am pretty sure that you can also carry in any quality chassis, for example a roller from Pete & Jakes for them to match up your body to. Others may be as good or better, but from what I have seen so far their approach is a pretty solid value for the dollars they charge.