Yes, excellent points, Thomas!
The absence of the items signed out by Berthier is especially disappointing given that so many key orders were issued under Berthier's name, not Napoleon's, owing to the GQG organization at the time. Your observation regarding the index is also true. :(
On the other hand, there is an enormous advantage in having all of the other material in one place--no need to acquire the seemingly endless array of "Lettres Inédites by Lecestre and others. :)