..I actually found out that the difference between a diagram 'opened' via
the new-diagram-wizard and via Project Explorer is that the EditorInput of
the opened editor in one case is instanceof FileEditorInput (if opened via
the Project Explorer) and in the other it is URIEditorInput (if opened via
the new-diagram-wizard).
It seems that if the EditorInput of the opened editor is of type
FileEditorInput it automatically reacts on the changes that the
sub-diagram does in it's 'doSave' method, so the "parent" diagram elements
automatically learn about the changes which are done by the sub-diagram
editor to the resource. However, this seems to NOT happen when using
URIEditorInput (which is, by the way, what GMF tools generate as per
standard, right!?)