Yeah, these boxes have always puzzled me.
First, I see them so often that I don’t think it’s random chance. Surely the HVAC trade isn’t THAT boring. Maybe it’s just a way they have of disposing the “oops” boxes, where they removed the wrong KO.
My first thoughts went to “ventilation,” but there’s nothing inside to ventilate! The one thing that might get warm — a box-mounted control transformer — hangs outside the box.