So, something like this, then--kind of sloppy since I didn't bother to precisely align things. A 0-height room with no roof that matches the size of the "windows," and then a doorway as the opening, and you get an atrium nook.
How hard would it have been for them to add a paragraph to the help file on this? It's totally non-obvious what you're supposed to do.
Thanks again.
AtriumExample.plan