I’m not able to explain why the writer wasn’t forced to have a very regular cipher which machines generate. But all I will say here are the past results, that can create sentence and the rest of main story.
You have a primary set of words, for example, f99r, first line
P.A’. T. D.S. V, D.P.T.D.S.V, S.A.M, P’A. T. T. V, P.J.D.T’, S.A.T’, GA.T. D. T’
Now if the repetition be removed, it will become
P.A’, D.P, S.A.M, P’A. T. V , P.J.D, S. A, GA.T. D
And if I change the script
با دب شام پاتو و پجد سا قاتد
I can read some parts clearly and some parts with help of last pages.
پجد ساقا
This is the clear part pajad sagha , todays version is pazad sagheh meaning the stem cooks.
And from this I will tell you how the whole stuff was created.
1. Primary words were seen without space, separated into pieces. The pieces don’t seem very regular, like when you think it is three letters long, it has many varieties.
P.A’, D.P, S.A.M, P’A. T. V , P.J.D, S. A, GA.T. D
2, 2, 3, 4, 3, 2, 4
2. Some regions of these were selected, and those regions were the place for next step:
P.A’, D.P, S.A.M, P’A. T. V, P.J.D, S. A, GA.T. D
3. Some segments were added, with regular rules, layer by layer, why? Because in many pages if you delete them, other segments will be visible.
P.A’. T. D.S. V, D.P.T.D.S.V, S.A.M, P’A. T. T. V, P.J.D.T’, S.A.T’, GA.T. D. T’
4. Now it is time to make it even more illegible, how? Change the letters into mysterious form. One letter is not shown with two voynich signs, in fact it is opposite: two letters are shown with one voynich sign. As it is clear for PA, GA, etc.
And the shape also had been changed.