The reason for angle in the stock mounts is that the axle moves forward and back as the spring compresses. The shock bushings can twist around the bolts/sleeves to compensate for this. If you turn the shock mounts perpendicular to the way they are supposed to be (like in pictures of Avery's rear suspension above), then all of that movement has to happen by squishing the shock eye bushings. Once you limit them out, you will bend stuff. When the suspension is really flexy, the axle does move side to side a little during articulation, so there is no way to avoid this problem entirely while still using stock-type bushings to mount the shocks, but the factory arrangement has the bolts at good angles to account for some of this movement at the top and some at the bottom (not that the factory suspension can move much).
That being said, many of us use the Ford shock towers in the front without any issues, but the lower mount is still in the correct orientation.