I have a 07/2004 3.0d and I recently had a failed front dif. Therefore, I had to take the front shaft down, among the other cute things you have to do when replacing the front dif. Since I was worried about the splines too (around 70k miles on the X by now), I took a look at them. I admit I haven't actually measured the length of the shaft splines vs. the length of the TC output splines, but judging by the eye, they were pretty much the same length. I expected the coupler to be like double the length, or something, like the picture amacman posted in post #3, so that it made sense to have a longer shaft spline.
On the other hand, making the shaft out of a better metal compound, like you said, should help.

Overall, after getting around the whole transmission system of the X and looking at its so many weak points (TC chain stretching, TC actuator failures, splines corrosion, dif. failure, CV failures) and weird designs (front dif. passenger side going through the oil pan), I am kinda disappointed and I can't even imagine going soft off-road with the X, since it easily breaks down on the street already