Scott,
Think like a pixel. You are a red, green or blue one and you have perfectly corresponding pixels in each image raw image. If one image is shifted (before being deBayered) relative to another, as would occur in star alignment, then all the pixels of the same color do not line up, and the stack cannot be deBayered. So, simply, any operation that shifts the pixels around must be applied after deBayering. Furthermore, it is safest to crop after deBayering. The deBayering algorithms expect a certain color pixel in the first spot, and an even number of pixels--at least the algorithm with which I am familiar.
Cheers,
Alex W