Well from what I understand about stitching is you need pixels and RAWs are not really pixels until they have been processed. The bayer pattern has nothing to do with it. The photomerge applications look for matching pixels and then makes decisions what to use and throw out regarding the stitch. As I said in the article look at the layers and click the eye button to make layers visible or not and see the way the program has decided to use pieces of the image. Since a RAW file is just data it would be very hard to do.
Also, as I mention in the article it is best to get as much from the RAW as possible prior to output. So, make adjustments on color, overall exposure, contrast and saturation, even a bit of highlight and shadow recovery prior to output. Do not crop, try any lens corrections or perspective corrections. Make sure the same corrections are applied to all images. This will certainly mess up the stitch. You can then as I showed do adjustments to tweak the look after the final file is complete.
Kevin Raber