The crucial fifth piece of evidence exists. It is in the Traité d'accompagnement, the anonymous treatise to which the Lilly autograph is appended.
The unidentified author of the Traité says it three times, in three different ways: Charpentier wrote that little manuscript.
The first allusion to Charpentier's authorship appears on page 18.(45) In the left-hand margin the author wrote: Principes de Charpentier, Ière Regle, Point d'harmonie sans tierce à plusieurs parties, ou contre la basse. This "first rule" is actually an amalgam of the brief rule at the top of folio 1 recto of the Lilly autograph (Point d'harmonie sans tierce), and the first point in the final "recapitulation" on folio 6 verso that ends the Lilly manuscript (Faites tierce contre la basse ou entre les parties, autrement point d'harmonie). In other words, the author knew full well that the little manuscript was by Marc-Antoine Charpentier. (Note that he called the manuscript "Principes," a title that calls to mind Loulié's Élements ou Principes.)
The second mention of Charpentier is found on page 20: La quarte consonance se pratique encore encore les parties, sans estre liée, ny sauvée. C'estoit l'opinion de feu Charpentier. Here the author of the Traité was quoting quite accurately folio 4 recto of the Lilly autograph: La Quarte considerée comme consonance se pratique entre les parties sans estre liée ny sauvée ... To be precise, first he quoted a point made in the autograph, and then he asserted that this was "the late Charpentier's opinion." Quoting from the manuscript and attributing the quotation to Charpentier is tantamount to stating, albeit somewhat less overtly, that Charpentier was the author of manuscript "XLI."
The final allusion to Charpentier comes on page 26. There the unidentified author describes a pedagogical technique that Charpentier and Loulié had both used when teaching accompaniment to beginners. And the anonyous author's words offer the proof for which I have been searching: Ces observations sont reçues dans touts les Traitez de composition, et je les tiens de Charpentier et de Loulier [sic]. "... I got [the information about this practice] from Charpentier and Loulié"! In that forthcoming Musing, It is essential to note that the practice to which he is referring is not discussed in manuscript "XLI" nor in Loulié's published treatises; but there is an allusion to it in one of Loulié's manuscripts.
This assertion that "I got it from Charpentier and Loulié" can mean only one thing: the author of the Traité knew the two men personally, and he discussed keyboard pedagogy with them. That more or less explains how the Lilly autograph came into the possession of the author of the Traité: Charpentier either gave it to him, or else Charpentier's heirs did so shortly after his death in early 1704.
The three statements in the Traité d'accompagnement prove Charpentier's authorship of the Lilly autograph, just as Loulié's attribution proves Charpentier's authorship of the Règles.
That is to say, in both instances someone who knew Charpentier
personally, attributed a theoretical manuscript to him. In neither case
is the attribution based on hearsay. It is based on personal contact
with Marc-Antoine Charpentier, and on familiarity with his work as a
teacher and a theorist.
In conclusion, I believe I have demonstrated that manuscript "XLI" was drafted by Charpentier himself, and then was copied out by him personally, in the fall of 1698. And thanks to the illustrations authorized by the Lilly Library, I believe I have made a first step toward understanding just how the Règles and the Augmentations add depth and an overarching significance to the autograph manuscript owned by the Library.
I wish musical-theory geologists many exciting expeditions into the unexplored regions of the different strata of Charpentier's theoretical production! I have looked at these strata all too superficially here, because my competence in musical theory is woefully inferior to that demonstrated by the adolescent Duke of Chartres back in the early 1690s.
45. The page numbering early in the Traité is rather chaotic, but as best I could calculate, Charpentier is mentioned on pp. 18, 20, and 26.