The authorship of the Cipher Manuscript has never been established. I believe that it is only fairly recently, since Ellic Howe in the early 1970s perhaps, that there has been speculation about its authorship.
Mathers' damaging claim in 1900, which fatally fractured the Order, was that Westcott had forged the
correspondence between himself and Soror S.D.A. in Germany (see
Equinox I,3, pp. 255 and following), not that he had written the Cipher Manuscript. This was to bolster his claim that only he was in authentic communication with the Secret Chiefs, and receiving new information about the Order.
As far as I know, no one at the time ever accused either man, or the deceased Woodman, of having written the document. Although both Westcott and Mathers undoubtedly had the learning, it is clear that they followed Levi's Hebrew letter - Tarot trump associations as late as 1887 and 1888 respectively (Westcott in
Tabula Bembina; The Isiac Tablet of Cardinal Bembo,
http://www.sacred-texts.com/eso/isi/isi02.htm - (bottom of page);
Mathers,
The Tarot: Its Occult Significance, Use in Fortune-Telling, Method of Play, Etc. -
http://sacred-texts.com/tarot/mathers/mtar01.htm - (table at bottom of page))
The discovery of the Cipher Manuscript after Mackenzie's death in 1886, and the decision to found an Order based on it clearly convinced both men of the other, secret system revealed there. It seems unlikely that both of them would have so openly published a wrong Hebrew letter Tarot trump association if they knew otherwise at the time, or if either to them were the author of the system.
Crowley's own opinion about claims of forgery or recent composition, etc. is of the "the proof of the pudding is in the eating" variety: it doesn't matter who made it, just that if it works, if it is beautiful, if it is inspired, then it is worthy to be held in higher esteem than a banal truth ("Of All Truth", rather than "Certain withot error"). It's the same as he argued for Einstein's theory of Relativity, or the question of the origin of Tarot itself. He states it in the following way in
Liber LXI, "The History Lection", verse 7:
"Some years ago a number of cipher MSS. were discovered and deciphered by certain students. They attracted much attention, as they purported to derive from the Rosicrucians. You will readily understand that
the genuineness of the claim matters no whit, such literature being judged by itself, not by its purported sources."
Crowley offers arguments for Levi having known the document on pp. 6-7 of
The Book of Thoth, but I don't think they stand up to scrutiny.