Let’s take a look at what was happening back in the 15th Century, which is when, with all probability, the manuscript was created.
The Ottoman Empire had conquered Constantinople in 1453, thus increasing the importance of Islam.
For the Christian Church, a major power that adopted another religion than Christianity as pretty much a state religion was especially threatening. So Christian religious communities were particularly keen to propagate the barbarous heathen infidel image of the Ottomans (Turks) and keep the faithful believing this.
From our present point of view, the important thing to note is that the Turks used Arabic script for their documents. In that, books from their cultural area were made suspicious for the Christians.
In 1455 pope Callixtus III urged a crusade against the Turks.
Apart from that, the Spanish Inquisition reared its ugly head in 1478. During the Inquisition, both Hebraic and Arabic books were put to the torchset fire.
A woeful climax was reached in 1499, when Cardinal Francisco Jiménez ordered 80‘000 books to be burnt in Granada and proclaimed Arabic to be the language of a heretical and despicable race.
Arabic books, especially of a theological nature, were endangered during this period.
This was probably the reason why Arabic scribes, to save their works, came up with the idea of encoding books (only one is known, which is what we’re discussing here) at multiple levels with strange glyphs, so that they didn’t appear to be Arabic (or Hebraic) at all and could thus avoid being destroyed.
Judging by the complexity of the manuscript, it was certainly not intended that outsiders would be able to decode it, but that the authors alone would be in a position to restore their original text.