Been following your progress and it's looking great. Being a carpenter's wife, I love looking at work-in-progress. If I understand your cabinet / duct work correctly, he's going to butt the cabinets close to the duct work but not covering them. Then cover the duct work. This would leave a small gap between the wall and the cabinets. A suggestion might be putting a couple of shelves in that empty space. Then it would look like it was planned.
Just a thought. Looking great -- can't wait to see the finished room!!!