I didn't think of the output shaft (drive shaft) geometry thing.
Of course if you've got the space or are willing to BFH the floor you could just put a spacer under the trans mount, gain ground clearance and get both pinions, the tcase and the transfer case to be parallel (or really darn close).
How does the DC yoke being short affect vibration potential? All I can think of is that compared to a drive shaft it's got a whole lot less mass to accelerate/decelerate over the course of a rotation therefore making less vibration even though the shaft is still slowing down and speeding up so for a given amount of vibration it can be a whole lot more out of phase than a drive shaft. Hoverer, if it's out of phase won't it slow down and speed up everything down stream of it?
I don't see the problem with welded flanges. They're welded into tube to build a drive shaft. Welding them to each other just skips the middle man.