From the Fujifilm X-Pro 1 manual:
When AREA is selected for AF MODE in the shooting menu and S is selected for focus mode, the electronic viewfinder and LCD monitor offer a choice of 49 focus points and the optical viewfinder a choice of 25, allowing photographs to be composed with the main subject positioned almost anywhere in the frame.
What is the reason for this limitation in the optical finder? In either case, the main sensor is used to for contrast-detect focus, so there doesn't seem to be an inherent restriction. Is it just because the parallax of the optical finder inherently introduces uncertainty, and so the optical mode forces larger focus areas to reduce the risk?