Stu--
the reason the 40mm lens is bringing up 50mm framelines in additional to the 40mm ones is pretty simple. The M bayonet mount is "coded" to bring up sets of framelines, originally on Leica M bodies. Three different "codes" were introduced for three different pairs of framelines: 28/90, 50/75, and 35/135. Unless I'm missing something, all lenses developed for Leica M bodies correspond to one of these focal lengths. I assume the reason they will also bring up framelines for a different focal length (assuming the viewfinder is equipped with those framelines) is that it would have been too complicated to program six different "codes" into the bayonet mount.
When the Leica CL and its 40mm lens were introduced, rather than reinventing the wheel (read: M mount), I gather that the engineers at Wetzlar were faced with the choice of coding the 40mm lens mount for 35/135 or 50/75. (The corresponding 40mm framelines are permanently visible in the CL's viewfinder.) For some reason, they opted for the 50/75 mount, which is why you also see 50mm framelines when mounting your 40mm lens. (Since the CL viewfinder is not equipped with 75mm framelines, those are not shown.) Had they opted for the 35/135 mount, you would only be seeing the appropriate 40mm framelines in your viewfinder, since the CL viewfinder is not equipped with either 35mm or 135mm framelines, either.
If you are bugged by this, you can effectively turn your lens's 50/75 mount into a 35/135 mount by filing away a bit of the mount. I know someone who has successfully done this, but please don't attempt it without precise instructions on where to file away. Googling for this might produce some results. Good luck.