You want the centerline axis of the rear-end input shaft to be parallel to the centerline axis of the transmission output shaft. The transmission doesn't need to point directly at the rear end input shaft.

By placing the centerlines of the rear-end and the transmission parallel to each other, the front u-joint will have the same angle as the rear u-joint. This will provide the least amount of torsional vibration in the drivetrain, and the quietest ride.