This is not 100% true. It saves the layout. However if you have toolbars in an external .rui and you close that .rui, restoring a window layout saved while the .rui was open will not bring back the tools in the closed .rui - because it does not contain them. If you re-open the .rui then restoring the window layout will put the toolbars back where they were when the window layout was last saved.
Tested in this thread (particularly post #10)