List of various peculiarities of the Voynich Manuscript and how they could be explained under the prisoner scenario:
1) Use of a very strong cipher and not providing the key or any clues: The risk for the author if the manuscript is discovered by the guards and attributed to the author was not loss of some secrets or some vague problems, but possible death penalty for the violation of the conditions of the imprisonment.
2) Use of a custom script and lack of any plaintext inscriptions: To make it impossible to identify the author by matching the handwriting.
3) Varying color of the ink, mistakes in the alignment of the text, occasional weirdly shaped glyphs, mistakes in illustrations, signs of bad quality writing tools, despite visible proficiency with the quill: To avoid being discovered, the author often had to write under low light conditions (moonlight, vigil candle), in an uncomfortable position or on a surface not very suitable for this kind of work, using low quantities or makeshift low quality (diluted?) ink and writing tools.
4) Using vellum and durable inks: The author was possibly sentenced for decades, had no idea when and how it would be possible to pass the manuscript outside, the folios had to be stashed for years in places with possible adverse conditions: moisture, temperature, insects. It had to be durable to survive.
5) Strange images none of which can be easily and unambiguously explained: All the images are decoys to make the manuscript interesting enough to warrant eventual deciphering by whoever finds it. If that was the calculation of the author, it fully worked, according to the most common understanding the manuscript has passed through court(s), went to Rome and ended up as one of the most famous manuscripts in the world. Under the prisoner scenario this is exactly what the images were designed for: to make the MS stand out.
6) Unknown plants, images that somewhat mimic images in other manuscripts, but not exact copies and with many details altered: while imprisoned the author had no access to other manuscripts, plant samples or herbals. If a non biologist is tasked to create a hundred intriguing decoy plan images, it's quite likely that the result will be similar to the Voynich MS with many striking shapes, unrealistic details and no way to perfectly match with any real plant.
7) Foldouts, Rosettes: they are one of the best attention grabbers, something that any person holding the manuscript would probably notice even without opening the MS. The largest foldout has a very intriguing design.
8) Several scribes/hands: this one if true is probably incompatible with the prisoner scenario, even though in principle there could be several accomplices. On the other hand, it's not impossible to explain the simultaneous variation of the statistics of the text and the handwriting if some cipher that restricts the positions of glyphs was used, see an example: You are not allowed to view links.
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9) Small format of the MS: the folios had to remain well hidden in close quarters most of the time. Also, if the intention was to eventually smuggle it outside, the smaller the better.
10) Unusually long for a cipher manuscript: time was one thing that the author had in abundance.
11) Lack of original provenance: this is by design, there should have been no link to the original author.
12) Weird marginalia: other than adding to the intrigue of the manuscript there is also some the possibility that one of the confidants of the author was a local book dealer/collector that would certainly be attracted to a new strange ciphered manuscript of unknown origin discovered in the region, if it's put for sale. Maybe marginalia has some references or connotations that would only be obvious to this particular person. Maybe "michiton oladabas" is a nonsensical message that somehow would ring the bell for one person only, the person who would be the most likely to know who was the author and how to decipher the manuscript. Distorted letters from You are not allowed to view links.
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Login to view. could be an attempt of the original author to disguise own handwriting while writing in the Latin script. Maybe You are not allowed to view links.
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Login to view. is the key, just expressed in a way that only someone would understand.
13) Weird paint job: possibly not original, it's unlikely the prisoner as described above would have had access to raw materials to create paints (except red, which under this scenario was obviously used by the original author on f67r2). Under the prisoner scenario it's likely the manuscript wasn't given by the author to the next owner, but was discovered by the next owner independently and without any knowledge of the manuscript contents, so maybe the paint job was this second owner's way of completing the manuscript to make it more pretty or just a pastime. There are some probable coloring instructions though, I'm not sure who would have added them and when under the prisoner scenario.
14) Wrong order of folios: maybe the original manuscript was never bound at all by the author, due to the lack of tools and materials, and it was discovered by the next owner as a stack of bifolios.
15) Tiny glyphs: this is folk psychology, but anecdotally when writing in secret and avoiding surveillance people tend to write smaller, due to increased tension in muscles. Also stress may cause transient tremors that could explain some irregularities in the text in addition to 2) above. Also see the link in 8) above, it could be possible that the cipher put restrictions on the positions and sizes of the letters.
16) Dubious geometry like wobbly circles, bad segmentation, lack of lining: the author simply had no good tools for this, but wanted to create striking visuals nevertheless.