Many of us want to reorganize Idle from multiple windows, some with menus, to one window with multiple frame or panes.  The initial steps: 

a) create a new application window with an application menu. (I believe OSX partially forces this on Macs anyway.) The menu should have items added or deleted, or just activated or not, according to the active window and other conditions. Adjust the menu construction functions, including the ones used in extension files, accordingly.

b) remove the menu and Toplevel from the base editor window used for editor, shell, and output.  Leave frame that can be added to other containers, whether Toplevel, Frame, Paned Window, or Notebook.

c) remove the Toplevel from dialogs that we think should be non-modal and insertable into containers.  I think the debugger, as you say, aumented config dialog, and improved search/replace dialog, are all candidates for this treatment.

I think users, or at least class instructors, should have some control over placement.  There definitely should not be a single, locked down design.