1) Maybe the reason FWD automobile splines don't fail from manufacturing errors (per post 34 by jconway607 of the referenced thread) is the slight radial compliance of the clutch damper spring system. Our bikes have no torsional damper springs, but instead only a flex plate which is probably radially a lot stiffer. As a result we are probably a lot more sensitive to clutch housing manufacturing errors.
2) I think ferrous oxide (the grey wear debris stuff inside failing clutch housings) is still magnetic, but clutch disk wear products are probably not. If so, sweeping the area around the spline with a magnet with the starter removed would show the relative quality of the alignment-caused wear a particular bike. At least it might be better than simply a visual evaluation.
3) Just maybe there is a greater clutch spline wear contribution from the crankshaft main bearing clearance than we have been realizing. Do you check for rear main bearing clearance in all radial directions when you find a bad spline system? I read in the Pelican Parts site post by Bill Pierce that he only saw like .0015" clearance. I wonder if he misread the indicator (unlikely given the quality of the rest of his posts) or if he didn't happen to check in the worst direction?
When I did my sole spline failure forensics, I found reasonable main bearing clearance in one axis, but over .007" in an odd direction - sort of like the bearing shell was worn in a race track or oval manner. It didn't require a dial indicator as the clunk would have been obvious to anyone handling the screwdriver pry bar.
4) (edit) I tried keeping the transmission slightly loose (as I proposed in a post in the referenced string) from the engine when I re-did spline lube on my R90/6 a year ago. There was a quite perceptible "breathing" between the two whenever the clutch was let out, but I was unable to find a happier combination that allowed the transmission to align any better with the engine.
You are correct that maybe I should have said I don't understand how these splines wear, but I know gear theory (splines are a subset of gears), manufacturing practices, and failure forensics from elsewhere, including the school of very hard knocks.