Another factor to consider is that starting with version 0.6, Shotwell will allow the user to import RAW files from cameras. If the user edits a RAW photo in Shotwell, we cannot update the RAW file with those changes; only cameras can write RAW data. So even if we go with approach (B) above, for every RAW master file all changes would need to be written to a separate JPEG photo file, presumably in the same directory as the RAW master.
Another factor to consider is that starting with version 0.6, Shotwell will allow the user to import RAW files from cameras. If the user edits a RAW photo in Shotwell, we cannot update the RAW file with those changes; only cameras can write RAW data. So even if we go with approach (B) above, for every RAW master file all changes would need to be written to a separate JPEG photo file, presumably in the same directory as the RAW master.