The only way I was able to get it to look correctly was to use a "material region", which I drew over the entire floor and notched out the section over the stairs.
I thought perhaps it was a framing issue so I tried turning off the framing inside the walls - no luck. Next I tried to make the materials for the wall 'air gap' - No luck there either.
I'll keep playing around with it, but for now - try using 'material region' and see if it gives you the look I was able to achieve.
Note: I'm currently using X14 for this example.
The best approach would be to turn your interior walls to partition. This will keep them from cutting through the floor. Your model has some errors in it; so when you do this you may still see the floor being cut at the closet just inside the front bedroom. This is because your floor in this one closet is higher than the rest of the floor on the second floor.
This is an issue with PBR's refractions. I run into it all the time when I try to do a PBR on a room and have used 2D plants on the exterior. They won't show up through the glass. It's an issue @ChiefArchitecthas been asked about (at least from me); so I'm hoping for a solution soon. If you turn off 'refractions' in your PBR settings I'm sure it'll come through, but it won't look as 'nice and realistic'