Caution, I have my HVAC hat on.
As a design issue I would want the box sealed to the plenum air, just so it does not become part of the return venting system and pack with dirt. George's idea of the metal deflector would work but you are also compromising the effectiveness of that plenum for returning air. If the HVAC guy computed that he needed a 14.5 x 3.5 duct, you have just choked that down to 11 or 12 inches and if it is not a smooth transition the turbulence effect makes it worse than that.
I doubt they really slice things that finely in residential systems but I also think they are likely to err on the small side most of the time and make ducts smaller than they should be. This will only make that worse.
I agree the electrical code may be somewhat ambiguous on this but you could have an HVAC issue.
