Normals should be okay by default. I suspect there is some limitation in blender or the plugin. Sometimes simple brushes connect in a way that breaks the script. Other times I get a very thin layer on one side of the substracted doorway for example and cannot place a floor under. With some tweaking they work. I will leave the rest for post-edit.
As for the window problem I do not know what was the cause but I remade the whole thing and now it works nicely. I have to admire the simplicity of creating free-form window sockets.
