Re: how to remove floor without roof clipping through the walls ?
Tbh, I don't think you can do what you are trying to do because of the octagon roof and the way it interacts with fences and floor openings. What is really needed in build mode for octagon (and the other non-square roofs) is sections like we have for regular square and rectangular roofs, so they don't have to intrude into spaces like you're trying to create but we don't have them.
Usually, the way to get an open stair is figure out where it lands on the upper floor, then fence in the area you want open, delete the floor inside the opening and place the stairs in the right position below. But with octagon roofs, what happens is that it ignores the fence inside and thinks the space is open to the outside and intrudes into the space, wiping out every object in that space and makes it unusable. To stop the intrusion, you have to use full walls around the stair which in your case, I don't think will work since you can't place the stair as the wall section won't let you land the stair by auto deleting like a fence section does. Changing the fence to a half wall gives you the same thing too. Only a full wall will keep the octagon roof from intruding.
The one thing I think might work in your case is forget the open section and fencing. As soon as you try to use a fence, the octagon roof will intrude but the stairs alone might work. Another thing you could try is using a ladder instead of a stair, again forgetting the open stair concept.
Hope this helps.
