It’s going to be all about airflow - discharge area and return area. The Atwood furnace installation instructions have a minimum duct work discharge area and CFM as well as a minimum return air area. If they are not met then the unit can overheat. Since your furnace looks to be in the slide there are only so many locations to get the required airflow hence the 2 ducts in the same location. I would be careful taking away any of the return area by moving a duct on the return grill.
IMHO the damper vents are your best bet.
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