In a little more detail: the Smalltalk MVC (model-view-controller) GUI had an overlapping windows scheme, but only the topmost window is active. Since it is topmost, it isn't partially covered by any of the others and updating it is trivial. Clicking any other window brings it to the top and only then is it updated.
Switching between windows was a lightweight operation which gave Bill the wrong impression that even background windows were being updated. That would have required clipping graphics operations by arbitrary shapes, which Smalltalk didn't do.
Bill spent a while figuring out how to do that and as a side effect could easily implement non rectangular windows, like the rounded corners that Steve Jobs wanted.