When your camera is in raw mode, the camera generates the full raw file (color image, full size) no matter what in-camera processing settings you have enabled. Some post-processing software recognizes the flags in the file that indicate what settings were used and initially display the file in your raw app — and you might initially see it cropped, in monochrome, or something else. (There was recently a related discussion in a thread about the DR100, DR200, and DR400 settings on Fujifilm cameras.)
When you work in the camera’s jpg mode the in-camera settings are (unless there are exceptions I don’t know about) “hard-wired” into the file jpg file that you get from the camera. Bit depth decreases, cropping and color and sharpening and luminosity changes are a permanent part of the file and cannot be “turned off.”
Most probably know this, but it is probably worth pointing out that this is not unique to Fujifilm. For example, my other system is from Canon. I essentially always use raw mode on that system, but I also prefer a different crop than the native 3:2 ratio. When I import files into Adobe Bridge and open them in ACR they initially show the 4:3 aspect ratio area that I set in camera, but the full 3:2 files is there and easy to access.
