I wish someone w/optical expertise like Brian Sweeney were here to explain it themselves, but I think he did a good job in this thread:
http://www.rangefinderforum.com/forums/showthread.php?t=59603
And Dante Stella touches on many of the same issues here:
http://www.dantestella.com/technical/compat.html
My understanding of why the focal length difference matters, even a difference of less than 1mm, is that: (1) it directly affects the distance from the film plane that the normal lens has to move from closest focus to infinity focus; & (2) that distance is, in turn, effectively enshrined in the RF mechanism because it is standardized around the normal lens. As Mr. Stella noted in his article, the RF mechanism in all Leicas are built around the 51.6mm standard--while an individual "50mm" lens may vary from this standard focal length, adjustments are made w/shims, etc. in the lens itself to ensure that both the optics focus correctly from closest focus distance to infinity & that the entire focus range is accurately translated by the RF mechanism (e.g., Mr. Stella's reference to the special mounts for the DR Summicrons). The key point is, as Mr. Stella writes, that "the camera body does not know the focal length of the lens mounted." On wides & telephotos, the adjustments get more elaborate, but the idea is the same; the helicals & cams are made to ensure that the RF pickup moves the exact same distance as that on a normal lens, even though the optics may move a lot more or less relative to the film plane than a normal lens would.
The same principles apply to a Contax (or Contax-style system like the Nikon), i.e., the optical unit must move a certain distance from the film plane between closest focus & infinity & the RF is calibrated to that range of distances, w/the only difference being that the helical for the "50mm" lens is built into every camera body. The in-lens adjustments for wides & teles have to do the same thing that their Leica counterparts do, only via the external bayonet helicals. I can only assume that variations in focal length between individual normal lenses were dealt w/by adjusting the optical units since they don't have their own helicals.
Just like a Leica body, a Contax (or Nikon) body thinks that every lens is a normal lens, but because of the focal length difference between the Leitz & Zeiss standards, the distance that the optical unit has to travel from closest focus distance to infinity is different. As Mr. Sweeney wrote in the thread, "[t]he distance that [a 51.6mm lens] moves from the film as it is focussed between 3ft and infinity is smaller than the distance that a 52.4mm lens moves when focussed between 3ft and infinity." Thus, because the "50mm" helical is built into every Contax & Nikon RF body, you have the difference in rotational angle (formerly thought to be pitch) between the 2 helicals, as seen in the visibly different focus scales between the 2 systems.
Chris
Vince, you raise the question that I do not know the exact answer to. I have read Bob's book and the quotes cited, but I cannot accept that a difference of a millimeter or less (or 1/50th of a millimeter) would result in the differences in focus that other users claim to have found. If a lens without a focusing mount goes into a helical and is at infinity, shouldn't it focus accurately at all distances? Or, is the external mount accurate at infinity, but the internal isn't? Or does focusing the internal mount lens give accurate focus for both Sonnars and Nikkors at measured distances, but not according to the rangefinders. In other words, if you would set both brands of lenses at three feet using a tape measure, they would agree, but the rangefinders would not?
Until I have my own Contax and run my own tests, I will not know for sure, but I do not believe the focal lengths were the real issue. Cheers, WES