A manufacturer has two options for increasing ISO sensitivity; either to order the sensor to increase its analog sensitivity, or after a picture is taken to tell the camera to amplify the image signal via algorithms at the RAW conversion stage.
Fujifilm decided to implement the second choice with the X100 and this processing action is normally invisible to the user.
As long as the algorithms used for the treatment are performing well, there is no real problem for the end user. As far as RAW measurements are concerned, the sensor’s maximum sensitivity is ISO 1000. That’s why none of our metrics goes further.