Supply and Return Issue
Very interesting situation billybob but not unusual.
Was the installing company a licensed contractor (i.e. a 'professional')?. In my state, HVAC must be installed by state licensed contractors and a dissatified customer can file a compliant with the licensing board. If your state has a licensing law, and the company was not licensed, you probably have a stronger position from which to file a compliant. However, in my state filing a compliant may hurt the installer, but provides no relief to the home owner unless the licensed contractor is required to correct poor work. Filing compliants against unlicensed companies does nothing for the home owner. The state cannot require an unlicensed company to do work.
Looking at the outside of a packaged unit and inline with the home, I always expect to find the supply on the right and the return on the left. Identifying a unit with this arrangement is not a problem.