If an istD is 6MP at 12bits per pixel this would be about 9MB of raw sensor data. The .PEF files are a little over 12MB in size. What information is contained in the additional ~3MB? Or is the file simply "padded" to 2 bytes per pixel?
The file *is* simply padded to two bytes per pixel. :-) Plus IIRC it contains a low-resolution JPEG version of the image for preview purposes.
S