Pinion offset: Typically, many production cars do not have centered engines. They're often offset toward the passenger side of the vehicle. To compensate, the pinion in these applications is also offset (for example, in some later-model Fords, the offset is just under 1.00 inch). That means the passenger-side axle is shorter than the driver-side axle. This is very common, almost standard. George Cathey at Pro Designs echoes that comment, but goes on to point out that the pinion should be centered in a race car application, or one where the driveshaft is very short. That means the housing is constructed in such a way that the offset is taken into consideration. The bottom line here is, it's not a good idea to the have the driveshaft angle skewed in the car.
Housing ends: When it comes to selecting housing ends, the rearend pros recommend you select the housing end based upon the brake system you plan on using. Mark Williams recommends using the big-bearing Ford end over the small-bearing Ford housing ends because they're a lot beefier and less prone to breakage.