They really are not noticeably longer, maybe 1/8". The big difference is the shape where the u-joint mounts. The XJ's is sort of squared off and the YJ is curved allowing it to handle higher angles with out binding.
Ok I got them both out and compared. The YJ yoke is longer at the yoke and not the splined shaft. It is more "open" than the XJ yoke. I see now how this can help a lifted XJ.