If the transmission output flange and the differential input flange rotate in non parallel planes, it may induce vibrations. It may seem that having everything perfectly aligned is the best option. However this causes the universal joints in the drive shaft to remain static relative to the rest of the shaft. The consequence is that the forces are always applied to the same points on the joints, inducing premature wear and play which in turn will induce ... vibrations. So, the solution is to have the trans output shaft and the differential pinion shaft slightly misaligned, though rotating on parallel axis. This will have the joints work a bit and ensure their longer life. This is despite having the w/shop manual recommending for alignment, if I remember well.
As mentioned before by others, sub-frame, engine and transmission mounts play a role, and the position of the running gear is usually fine tuned by adding shims under the trans mount if necessary. Worth checking also is the rear axle center mounts, especially the lower cylindrical one: when it goes bad the rear axle usually rotates upwards on the pinion side, modifying the rotation axis of the pinion shaft. Position of the rear axle relative to that same mount can also be adjusted, resulting with variations of the rotation axis.
If everything is in good nick and positioned as it should and vibrations are still there, then it may be a shaft balancing problem. To be noted that the shafts are balanced as complete units, and the position of the front part relative to the rear part must be maintained (i.e. splines should be marked when both parts are separated so as to put them back in the same position relative to each other). So if one suspects the vibration to be due to a balancing problem, it is worth trying shifting the position of the shafts relative to each other by moving them around the splines. A bit time consuming, but it can yield good results.
Not sure if all this is very clear, I can try to explain differently if needed. I looked into this quite extensively some years ago, as I had a vibration at highway speeds that was driving me crazy on an otherwise very well sorted W109 6.3.