When a piece of evidence stands only on multiple arbitrary assumptions, like this one does, it is at best a supporting piece of evidence in the background, and certainly not a smoking gun.
Why were there two copies being produced in the first place? This is the question we should start with if we want to figure out what was going on.
Joseph was commanded to have Oliver produce two copies of the Book of Mormon manuscript, and:
"In going to and from the office, he should always have a guard to attend him for the purpose of protecting the manuscript" and "a guard should be kept constantly on the watch, both night and day, about the house, to protect the manuscript from malicious persons, who would infest the house for the purpose of destroying it. All these things were strictly attended to, according to the commandment."Such concerns about malicious persons attempting to destroy the sacred records and manuscripts certainly would have been relevant in Kirtland in 1835, as well.
The larger context here is that Joseph's first 116 pages of translation were stolen from him, in a conspiracy against him, and he was never going to forget that.
What length would he have gone to, to safeguard the Abraham manuscript, then? At the time, Joseph was using code names to protect the lives of Church members - so, with a proper understanding of that precedent, the characters could have had a similar safeguarding effect.
Orson Pratt wrote, regarding the code names:
...the substitution of fictitious names for persons and places does not alter or destroy the sense or ideas contained in the revelations. But what the Prophet did in relation to this thing, was not of himself: he was dictated by the Holy Ghost to make these substitutions, for the time being, until it should be wisdom for the true names to appear...The characters in the left margins could have protected the sacred record by associating the text with a different roll. With the scribe's adapted Abraham vignettes on the Hor roll, it would be natural for people to assume the text for the manuscripts was also on that roll, thus setting up a natural safeguard protecting the actual roll containing the text. What lengths is Joseph Smith known to go to in order to protect a sacred document? He hid the Gold Plates in a barrel of beans. And in Kirtland, there was a real threat of mobs coming through and ransacking the papyri. Even in 1832, in his own personal journal account of his First Vision, Joseph encrypted certain sacred details by simply saying the heavens were opened to him, without elaborating, apparently to protect the information in case his journal got into the wrong hands. He wrote the account only a few short months after a mob broke into his home, unprovoked in the middle of the night, tarring and beating Joseph Smith, leaving him for dead and resulting in the death of his child.
Additionally, the characters in the margins add a certain uniformity to the two manuscripts, which could be pointed to in case one was altered, even as a safeguard against the scribes themselves altering them, as most of the scribes did later turn on Joseph Smith.
The characters likely were added later, rather than interrupting the translation process in order to add them at the start of each paragraph. Jeff Lindsay argues convincingly in a series of posts on his blog that the manuscripts we have were not even the original manuscript but were copies.
Of course, the characters may have even been added much, much later and for far more frivolous reasons. We don't know the story behind them. Some critics, like Dan Vogel, claim their interpretation is simply "obviously" the only logical one. Ironically, that is actually an appeal to bias, resorted to in light of their failure to construct a logical argument in support of their accusation.