The importance of the post of chief of staff, especially at the army level is generally overlooked.
French General Paul Thiebault, the author of the French staff manuals of 1800 and 1813 believed that the chief of staff was/is 'the central point of the grand operations of armies.'
The premier chief of staff of the period was Alexandre Berthier and he was the first of the great chief of staff in military history.
Perhaps the following may put Berthier's job as chief of staff and Major General of the Grande Armee more in perspective and much more accurately. Of course, ingrained attitudes and one's own study and perspective are hard to influence, as you have stated many times. Anyways, here are some reliable and interesting references on Berthier:
'Quite apart form his specialist training as a topographical engineer, he had knowledge and experience of staff work and furthermore a remarkable grasp of everything to do with war. He had also, above all else, the gift of writing a complete order and transmitting it with the utmost speed and clarity...No one could have better suited General Bonaparte, who wanted a man capable of relieving him of all detailed work, to understand him instantly and to foresee what he would need.' -Thiebault, 1796
'In my campaigns Berthier was always to be found in my carriage. During the journey I used to study the plans of the situation and the reports sent in, sketch out my plans for battle from them, and arrange the necessary moves. Berthier would watch me at work, and at the first stopping-place or rest, whether it was day or night, he made out the orders and arrangements with a method and an exactness that was truly admirable. For this work he was always ready and untiring. That was Berthier's special merit. It was very great and valuable, and no one else could have replaced Berthier. -Napoleon
'to know the country thoroughly; to be able to conduct a reconnaissance with skill; to superintend the transmission of orders promptly; to lay down the most complicated movements intelligibly, but in a few words and with simplicity; these are the leading qualifications which should distinguish an officer selected for the head of the staff.' -Napoleon
'to describe [Berthier] merely as l'expediteur des ordres de 'Empereur (his own phrase to Soult) is a gross underestimate both of the man and of the organization that he controlled. The Grande Armee, after all, was the first in history to radically decentralize the conduct of operations in the field and spread them over hundreds, later even thousands, of square miles of territory. Such a method of waging war required a two-way information transmission and processing system larger and more complex than anything preciously attempted, and this system it was Berthier's responsibility to manage...When Berthier was absent, moreover, as was the case during the 1815 Waterloo campaign, the resulting muddle was monumental and led directly to the Emperor's fall.' -Martin van Creveld
'in 1796 [Berthier] produced a Document sur le Service de l'Etat Major General a l'Armee des Alpes, which he sent to Paris in the hope that it would serve as a model for other armies. Berthier's document divided the responsibilities of the General Staff into four sections, each under an adjutant general...'Though each adjutant general (there should be four assisting the chief of staff) is resonsible for one particular part of the service, he must be informed about the state of business in general. Nobody can send out anything is his own name; everything must come from the chief of staff who is the central pivot of all operations. All correspondence is addressed to him; he signs everything; in case he is absent, he will issue special orders.'' (this last quote is from Berthier's instructions which can be found in Etude sur le Service d'Etat Major by de Philip-K) -Martin van Creveld
The following refers to the 1805 Ulm Campaign: 'The march towards the area of deployment thus presented problems of coordination and supply on a gigantic scale. It speaks volumes for the efficiency of Napoleon's chief of staff, Berthier, that he could start sending out his orders [Berthier's] on 25 August and report on them to the Emperor just 24 hours later...Under Berthier's master plan, the divisions forming the cavalry corps were the first to leave the Channel coast, which some of them started doing as early as 25 August. Then followed the infantry corps of Davout, Soult, Ney, and Lannes marching along three parallel routes arranged form north to south so that only the last two had to share a road between them...Within this general framework much initiative was left to the marshals, each of whom was to send his ordonnateur and commissionaries ahead in order to make the detailed arrangements.' -Martin van Creveld
'[Berthier] was the perfect Chief of Staff. Scarcely had the supreme commander's thought been formed than Berthier had grasped it, both wholly and in its nuances.' -Georges Blond
According to Ferdinand von Funck, who 'served both against and with Napoleon' and 'knew the marshals', Berthier was an officer of 'incredible talent...hard and irascible' but 'amendable to reasonable presentations.'
Berthier and his staff planned the crossing of the Alps in 1800, the movement of the Grande Armee from the Channel and into Germany in 1805; and the unprecedented concentration for the invasion of Russia in 1812.
I would contend that Napoleon's style of command made it difficult for Berthier to be chief of staff in the modern sense of the words, although I think to dismiss him as a mere chief clerk is a little ungenerous. Perhaps the best illustration of that is how badly Soult handled it in 1815. In that respect the work of Sephen M Beckett in publishing the Operations of the Armeé Du Nord material is fascinating.