The colors I'm referring to is the colors from the RAW conversion using a calibrated camera profile. I have found it often very difficult to make the same colors from the two cameras when shot in the exact same conditions. I'm absolutely certain this is caused by the differences in the Bayer filters.
It's actually from a variety of sources. Bayer spectral transmission being only one of them.
For instance each sensor has different native spectral sensitivity, and an IR filter with a steeper or shallower cut, or a higher or lower cut frequency can make a large difference as well. Even the use of black frame technology can inherently alter the color response characteristics of a camera. Lenses, likewise can have an influence on both color directly, and on image rendering characteristics that influence our perception of color.
Image quality comes from a chain of success elements, a partial list includes:
Lens coating > Lens elements > Aperture blade design > internal body coating > microlens > Anti aliasing filter (if present) > IR filter > sensor photo well > sensor read-out (heat-sinking and/or active cooling very important here) > path to A/D converter > A/D converter > (read-out of black calibration file from sensor recorded as adjunct to the image) > debayering algorithm > color engine > color profile > deconvolution / detail finding algorithm, noise reduction based on black calibration file > noise reduction based on image data > sharpening.