This is neither a theory nor an hypothesis. It’s certainly not a considered opinion. This is a passing thought which might be worth investigating sometime, by someone.
A recent post by Ellie Velinska suggests for the plant on folio 45v, Teucrium chamaedrys.
While I was leaving a comment there in which the name Gentile da Foligno came up, I recalled Barsch’s reference to that “virum bonum” – noble man. Gentile da Foligno certainly deserves that description. A highly regarded physician, he wrote advice about how to cope with the plague, and included a recipe for the cure-all known as Theriac or ‘Venetian treacle’.
How to treat and prevent outbreaks of Plague was still in the seventeenth century a problem which exercised anyone interested in medicine. Still, after three centuries, it continued to surge and decline in Europe.
So perhaps what Barsch hoped for was some ‘ancient medicine’ as perfect cure-all or “theriac”. Various versions of ‘theriac’ were known and they are older than the Christian era. Barsch, a man of his time, would expect that medical recipes would be more effective and “purer” the more ancient they were. He seems also to have supposed his ‘Egyptian medicine’ more refined (‘alchemical’).
But if Barsch knew so much about the unreadable content of the manuscript, why did he not offer the name of any person as previous owner, as original composer etc.etc.? Still more to the point, since we could posit some financial interest on Barsch’s part ~ why did neither Marci or Kinner, nor any from among that circle of people linked to Horcicky and to Barsch at Prague and (in some cases) at Rome ever offer an explanation about the manuscript’s origins and history.. so far as we know from the extant correspondence.
I simply cannot believe the ‘Rudolf’ owned it story. For an Emperor to have owned and then conferred such a thing on anyone, let alone on a parentless waif such as Horcicky was, would be so remarkable that the tale would be told and retold by those who knew, as a marvellous thing. How could you not associate the Emperor with such a strange object whenever writing of it, or showing, giving or bequeathing it? No – it beggars belief that such a thing could be forgotten, even by Marci and Kinner.
I daresay we’ll never know who is responsible for first collating the various extracts, or for ordering (or himself making) the fifteenth century copy. (the two might be the same, of course).
But there is surely enough in the manuscript to argue that many of Barsch’s “hypothetical remarks” in his letter to Kircher are based in real knowledge – including his belief of connection to Egypt.
Of Theriac recipes.
Barsch surely knew two such “cure-alls” from Galen’s writings, where that known as Mithridatium is described by 41 ingredients and the Galene of Andromachus by 55. 
 (De Theriaca ad PampliiL init. vol. xiv
According to J.P Griffin, theriac was being made in commercial quantities by the twelfth century [erroneous ref. to Genoa deleted 27/03/2015]:
theriac was being manufactured in Venice and widely exported. In England it became known as Venetian treacle (‘treacle’ is a corruption of theriac). Theriac became an article of commerce, with Venice, Padua, Milan, Genoa, Bologna, Constantinople and Cairo all competing. The manufacture of these theriacs took place in public, with much pomp and ceremony.
J P Griffin, ‘Venetian treacle and the foundation of medicines regulation’, Br J Clin Pharmacol. 2004 Sep; 58(3): 317–325. (online)
Presumably each of these cities had a slightly different recipe, though the idea of keeping a trade secret secret while producing it in public becomes difficult to imagine. I wonder whether any recipe exists for the medieval Egyptian theriac?
Of course, he might have been thinking of some even older medicine – such as Kyphi.
Kyphi is a genuinely ancient Egyptian recipe, mentioned in the Pyramid Texts. When our earliest written recipe for it occurs, I don’t know. A nice looking (commercial) site called ‘Alchemy works’ gives ingredients for the Kyphi of Dioscorides and that attributed (on that site) to Galen ( here).
‘Alchemy works’ considers Kyphi an incense; they have another recipe which is named ‘Edfu Kyphi‘ which might be worth reading. But all this comes with the caveat that ‘Alchemy works’ is selling stuff, so check assertions and recipes if you want to follow up on this.
If I had any reason to chase the idea, I’d probably start from Egyptian sources, comparing them with the Nestorian Book of Medicines, and with some of those Islamic dispensatories that I’ve mentioned here before.
I don’t chase notions, storylines, “ideas” or ‘theories’, so unless something clearly related to the subject comes up in the manuscript’s imagery, I doubt I’ll do more about it.
You may feel differently – so Lisa Manniche’s books should be helpful and there is certainly a wiki article: ‘Kyphi‘.
Back to how Plague was treated …
Christiane Nockels Fabbri, ‘Treating Medieval Plague: The Wonderful Virtues of Theriac’, Early Science and Medicine, Vol. 12, No. 3 (2007), pp. 247-283 (JSTOR).