Atwood requires a minimum of 30 square inches of unrestricted flow. A 3" duct is 7.06 square inches. Using those numbers, 5 fully open, unrestricted ducts would give 35.30 square inches.In theory any additional registers could be closed. It may not be necessary to totaly close of any registers, only restrict the flow, redirecting it to the desired location.
I would recommend checking the CFM at each register with a flow meter, then closing the desired register/s and check for increased flow at the unrestricted registers.
There are two safety features in the furnace. A sail switch, and high tempperature sensor, of which either can shut down the furnace.
Any good HVAC tech should have a flow meter and be able to test and balance the system.