Hi - I’m new here but think I can shed some light on this as a former X10 owner.
The X10 is an example of Fujifilm’s fondness for exotic image sensors. The EXR sensor used in the X10, nominally 12MP, actually consists of two 6MP Bayer arrays overlapped with each other and offset by one pixel vertically and horizontally. This needs special processing to generate a 12MP output image. The EXR RAF file actually contains two 6MP RAW bayer encoded images, which need to be processed and combined. Unfortunately I never found an open source RAW editing tool that could detect and combine both of the images to give 12MP, instead they just handle the first 6MP raw image in the file, which is what you are seeing here.
In some experiments I did manage to extract both 6MP images manually using a command-line raw processing tool (I forget the name now, sorry), but I didn’t have any clue how to combine them into the larger 12MP file with a higher resolution.
Sorry I don’t have an answer, but hopefully that explains why you are seeing this behaviour.
The X10 was (is) a lovely camera, but frustration with RAW processing was my main reason for abandoning it. Have fun anyway!