. . .
It's not about "misalignment". You don't just "align" the powertrain. All powertrains are "misaligned" and it is perfectly ok, as long as they are set up correctly.
There are some old threads on here that go into this in some depth. The gist of it is, as I recall:
The "perfect" alignment of transmission and differential has the transmission output shaft and differential input shaft at equal and opposite angles to each other. I think the transmission "should" be pointed up slightly, and the diff pointed down slightly. Then the changes in rotational speed as the driveshaft goes through the joint at each end are equal and opposite and cancel each other out. I gather this is called "in phase."
But in these cars the transmission angle is not "right" -- I think it is pointed down rather than up. Plus the differential rotates a bit. All of this causes "phasing" issues through the driveshaft that cause vibrations and that's why the stock driveshaft has the extra joint in the middle and the CV joints.
If I remember correctly, sqidd spent quite a bit of time trying to get his drivetrain lined up correctly and came to the conclusion that it was practically impossible due to the chassis, so the best way to deal with it is with CV joints.
But my memory is not the greatest so "your mileage may vary" ;-)