This may just be the way you're wording it but the pinion angle of the rear diff isn't supposed to be pointing directly at the t-case out put (I think). It should be pointing just a little higher so that the DC joint has room to angle downward and connect to the DS. There can't be any kinking of the DC set-up or more (or less) angle at either of the u-joints in it. I'm under the impression that everything has to be equally bisected or the DC will wobble a good bit especially at speed. The slip joint in the DS will compensate to some degree but , at normal ride height, everything should be spot on. A 4-link will hold that angle pretty well but introduces variation in pinion angle over compression/extension depending on how equal or unequal the upper and lower links are.
I would think that if your rear diff isn't centered you still have to aim the pinion at the right spot. You kind of have to pretend that "vertical" is actual rotated a few degrees to the left because your diff is on the right. Sort of tip your head to sight it correctly. I don't have a lot of experience with DC rear driveshafts so I'm probably just mixed up here. I can also see your point that with things off center the DC joint is really just a bunch of weight being flung around at an angle while gravity is pulling straight down.
Anyway, nice work overall. I'm sure you'll get it sorted.