If under "a trim remmenant at the boundary" you mean a horizontal stripe of another color, it's the slab. You need to apply to it the same color that the nearby walls have.
the windows (which span both stories), only penetrate the wall on the lower level and on the upper level seem to be embedded in the wall.
Even after adding a ceiling opening, the lower part of the room resides in one storey and the higher in another. Any of windows or doors cannot create an opening in more than one storey at the same time. What you can do is to place identical windows on each floor so that they look like two halves of a larger one.
Also, why is there not a way to trace an existing floor plan, such as those provided by the builders?
It's not an easy task. We'll add this feature when it's possible.