Something like that I think. Tolkein was a linguist who could and did invent new languages out of nothing. Not the first that could do it, I’m sure. Would be a nice way of keeping prying eyes from discovering what was in your papers.
This book has too many illustrations that are typical for alchemists. Anyone seeing the book would instantly report the fact to the nearest Inquisition office; besides, most people at that time couldn't read, so any common writing would be just as much Greek for them.
And as I mentioned earlier, it's a dangerous thing to have writings in an unknown language because the Inquisition would be quick to conclude that the language is of Devil, and it is its holy task to torture you until you reveal it. If there is nothing to reveal ... too bad for you.
The cipher, if real, is also too hard. Even Leonardo simply wrote with his left hand and read the writing in the mirror. It's fairly easy, I can write this way and I'm sure everyone can. But this manuscript is written in a nearly perfect cipher. It is not necessary to have such a complex code, since the book itself - the posession, the illustrations, the code, etc. - is a far more damning evidence than anything that the text could possibly contain except, perhaps, the working secret of eternal life and such.
As I said earlier, my personal belief is that the manuscript was written for one purpose only - to be sold as an exotic, secret book to someone (an alchemist?) who could pay big bucks and was willing to decipher it. An alchemist close to the throne could pay kingly sums of money, literally. Any reasonably educated monk could do it easily, with access to writing implements and vellum and with knowledge of several alphabets. The words could be made up, one by one, and written on a piece of paper for reuse, and changed slightly where suffixes would normally be.