There's more to colours than simply three numbers. E.g., the colour separation (amount of "cross-talk" between colours) might be different between different detectors (I'm not saying it is for 5D and 5D2, just that it could be). The Bayer detector has three filters: R, G, & B. By making the filters broader in wavelength, you gain some sensitivity, but you also run the risk of having the filters overlap in wavelength and counting the same light twice, e.g. for both R and G, and that will decrease the colour fidelity in your image compared to filters where there is less overlap.I still preferred the colors out of my 5Dc than my MK3s. I skipped the mk2 series because it wasn't worth upgrading for me.I never understand comments like this. It is digital, why not profile your camera to get whatever "look" you want from it?
So, not all detectors necessarily reproduce colours the same way, and it is no possible to correct in software (because it would be an ill-posed inverse process).