Let me answer your questions.....as they are very valid.....
You are right, as I know what is the mechanism that leads up to the failure but not what started it in the first place as there are several bolted joints that can lead to the angular misalignment in question.....the easiest way to visualize the issue is if you look at a TV (top view) of the engine-tranny joint and consider that there is a vertical plane at the joints that will be mentioned below. This vertical plane has to be parallel to the next, within a small tolerance, that will not induce the premature wear of the mating components, i.e. the splines of the clutch disc and the splines of the tranny input shaft. I'll start from the engine and move back towards the tranny.....You offered a conclusion, but really no recommendation.
1) The center line of the crank
1) At the mating of the engine case with the transmission case
2) At the mating between the crank flange and the flywheel
3) At the mating between the flywheel and the pressure plate
4) At the mating of the transmission case and the mating of the engine case (this is the opposite from #1, as the vertical plane of the tranny could also be the problem)
5) The center line of the input shaft
Note that the point of flexion is between the clutch and the input shaft spline, so if the angular misalignment is on the clutch end the "gap" will be on the right side of the engine, if on the tranny side the "gap" will be on the left side......have I thoroughly confused you by now?
I had one and never was concerned about the problem, probably because if it happened to me I had CPO coverage and it would have been a challenge for me to get to the bottom of it. It does concern me that there have been sufficient number of failures to alert the OEM to a potential problem and they, for the most part, have ignored the issue. The failure will not cause you to wreck, thank God, if you are on a little traveled road but picture as to what could potentially be the outcome if you are on the slab at 80 mph in one of the middle or left lanes and all of a sudden you loose motive force.....would that be dangerous to your health?Are these bikes considered (by you) to be non-trustworthy?
I think I have answered all your questions......hopefully.......