This yoke alignment mystery has had me on the hop too. Let me really 'throw the cat amongst the pidgeons' here.
I have another car, a 1986 VL Calais built by GM-H [Aust.] equipped with a 6 cyl turbo and 4 spd auto which has the yokes in-line, but the exact same car in the 5 spd manual version has the yokes at 90 degrees!
Same diff and nose cone angle, same suspension, same shaft diameter and similar if not the same shaft length, yet totally opposing theroies on yoke alignment.
My nephew has a 5 spd manual version and it drives perfectly at all speeds and powers with the 90 deg offset shaft.
I have spoken to a few drive shaft specialists around the country and none of them can tell me why the manual VL has the yokes at 90 deg.
I've tried chasing GM about this but can't get past "level 1 support" as yet.
A couple of the driveshaft specialists did also mention that they had on file other GM-H cars with odd offsets like 20 deg and 33 deg. etc, though these may apply to cars with full IRS which may not have equal input/output included angles.
One thing that may need to be factored in to the theory is the shift in nose cone angle as the diff travels up and down, which is certainly the case with 4 coil suspension setups, so the whole thing with yoke alignment may be something of a 'best compromise', but 90 degrees is at the extreme and theoretically should compound the problem, not cancel it!! [Why did they do it and why does it work!!
I'm going to chase this mystery some more, if I get some answers I'll be sure to post back here.