If I remember right the alignment may not be an easy thing to figure out. when I looked at one a couple years ago while my reefer was being fixed (I had all day to kill), I thought about the frame and how it sits on the truck. looking at it carefully (I had all the covers off of it) and seeing how things are mounted, it looks like if the unit is aligned off the truck, and then placed on the truck. When the unit is bolted down on the mounts (frame), the sub-units like the A/C pump and generator may be moved just so slightly off center where they will tear up a belt.
Make sense?
I know another type, I forget the name, seems to have a metal welded frame that is attached to the truck frame and the three I seen being serviced were actually twisted so slightly.