Centered Rear End
The importance of centering your rear end depends totally on weather the third member (center section) is exposed or not. On cars that the rear end is very visible its best to center the rear housing in your chassis and shorten the axles accordingly to keep everything looking right. On full fendered cars or cars that you can not see the rear housing its okay to center the pinion to the drive shaft or trans output and wheels to the fenders.
Example: My sedan was built to show off the rear end because it originally had an IRS (Independent Rear Suspension) But I have recently replaced the IRS with a solid rear axle and I wanted the housing centered between the frame rails. The right axle tube, the longer one, needed to be shortened 3" and the left one 1" which left the center line of the round back 9" housing exactly in the middle. My friend has a full fendered 32 five window and his axle housings are basically stock( 68 Mustang 9") and his pinion is centered on the transmission output shaft. Mine is off set by about 1 1/2" to the right. Off setting the pinion to the trans output is okay as long as you phase the u-joints (keep them the same angle front to rear). I've seen some of the off road guys, rock climbers, who have as much as a 8" offset between the trans output and the pinion (side to side) but they phase the u-joints so they can drive at highway speeds without the harmonics (vibrations) associated with unphased drivelines.