Propshaft Bearings

[AustinWood]

Yes, they need to be aligned. As the shaft rotates, if it is not exactly inline, it is not in balance. By having them aligned the imbalance from either end cancels each other out.
To fully cancel out the imbalance the deflection on each joint must be the same. In fact this will not be the case with the Austin because the torque tube and the gearbox output shaft are not in line anyway. The error from this will be less than the error from having the UJs out of alignment.