My GUESS is that Canon might use a compressed TIFF format on the luminance data for each channel, i.e. a gray-scale image and add all kinds of information to it. Basic processing like dark current correction, compensation for non-linearity, etc. is already done before the file is compressed.
All evidence including the performane of the Phase One, Photoshop CS Raw, etc. converters is that the RAW converters are doing the bayer calculations and demosaicing. So they must be storing each RGGB layer separately.
Karen
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