There must be some misunderstanding here, CM is used as a launcher to replace the vanilla one. If content requires a custom shader like Stereo's ksPPMM_emissive included with the bmw, it'll still be needed when launched from vanilla launcher or CM.
Now, if you are also running CSP with CM (will also run without CM, but it'll then be impossible to configure patch related stuff without a proper gui), that's a different matter. Csp has some replacements for shaders that were needed to install separately on vanilla (very likely for that one). It's still a good idea to install their original version as a fallback nonetheless.