My understanding, and again, this could be wrong, is that the output of the t-case and the pinion need to be in the same plane, give or take some. If these two are too far out of alignment you may get driveline vibration. Again, my understanding here is limited, this is really my first foray into driveline and steering tech. Please correct me if this is not accurate or is too limited.
Interesting about the pinion gear splines, I was not aware of that. I'm not too worried about this though for my scenario. The face of my pinion flange is pointed 7 degrees towards my t-case with weight on the springs, I'm only running ~2" and I don't wheel this truck hard. For others with more lift or more horsepower this might be an issue.