AF is more precise, the later uses an area to derive optimal focusing. Practically the later method is faster. For AF method, one has to know which patch of the frame one can get a good focus distance so that takes a longer time.

This is actually quite simple: MF stands for MANUAL focus and was designed to be a 2-step-procedure: quickly pre-focus your target with the AFL button, then fine-tune the result using the focus ring in conjunction with the magnifier tool.

There is no AF frame visible in MF mode, hence nobody really knows the actual size of the AF frame that Fuji is using in MF/AFL mode.

The only visible frame there is the magnifier frame. Obviously, the active AF frame is somewhere in the center of the active magnifier frame, but we don't really know its exact size. I suppose it is the standard (medium) size of the 5 possible frame sizes you can select in AF-S.

Btw, XP1 offers higher magnification (and hence a smaller magnifier frame) than the X100, which in turn offers a smaller frame than the X10/X-S1.

If you also want to use the magnifier tool in AF-S with the X100, your wish may come true quicker than you think.