Peter is pointing to the fact that the Hooke type joint is not a constant velocity joint. If those two flanges are not all in one line, for example as the car bounces up and down, and assuming the rear axle rotational velocity is more or less constant, the center shaft actually speeds up and slows down twice for every revolution. The amount is dependent on the angle, or how much bounce in the car. The yokes are assembled parallel, and the gearbox shaft is more or less parallel to the axle shaft, so this non-constant rotation is cancelled out. If the front flange is not assembled with the yoke parallel to the rear, the engine will be forced to turn at a non-constant speed, i.e. speeding up and slowing down twice in every revolution. Thus you get vibration.
Failure to observe and follow these parallelism requirements is why some off-roaders and jacked-up pickup trucks go through a lot of u-joints.
Notice the two yokes are parallel in this picture from the Mark V Service Manual. Mine had a couple of arrows for alignment marks.
A Mark V has three u-joints.
This is the front shaft of the first type.
It has splines on the rear so it is possible to assemble the rear flange wrong. They tell you to mark it before taking it apart, but if you didn’t do that, you can figure out the correct way by looking at the second type.
On the second type, also used on Mark VII, the flange can be put on only two ways, both of which are correct. The yoke on the front drive shaft ends up parallel to the yokes of the rear drive shaft.
I wish I had taken better pictures of this feature before putting the body on, but they were all taken at the same time and the driveshaft was not turned. You can see the pairs of bolts close to each other, all 3 pairs in the same angular relation.