Is this what your trying to accomplish? I used HDP 2021 and cut the main roof on each side of dormer and moved middle section in front of Dormer back against the wall. That will turn off your auto build roof if you have it on.
I created a second floor which in your case would be third floor and set the floor height at 12" and the 12" window at -12" to Bottom. This is using HD 1021
I did these in Home Designer Pro 2021. Before lowering the ceiling I turned off Auto Build roof and the Ceiling dropped but the walls and Roof remained the same.