You can make, or have made, a transition that is 3" less in depth and wider to accommodate the door and soffit.
I would recommend having the transition built by someone who can calculate the correct dimensions using a ductulator so the airflow isn't compromised. The width may or may not have to be the same amount as the change in the difference in depth because this will depend on the dimensions of the existing duct.
"The physician can bury his mistakes, but the architect can only advise his clients to plant vines." -- Frank Lloyd Wright