I'm most certain it seems that way to you.
But the simple truth to the matter is that both your pamphlet author and your writer of the "unmarked" codes knew exactly what the order of the alleged ciphers was going to be before there was ever any order assigned to them. And that, my friend, is a cold and hard and undeniable fact. Only one possible way this could have transpired.
I've enjoyed reading this thread but i think there is actually a reasonable explanation that could be considered.
Let me start by saying that I have no horse in this race. I enjoy reading about the legend purely for entertainment and am certainly not a Beale researcher but I do enjoy probability puzzles.
On the surface your premise looks very sound however there are some things to consider. I don't agree that it is air tight proof that the cipher author and the pamphleteer are the same person.
A set of three papers (labeled 1,2,3) can be shuffled randomly and will have only 6 possible resulting combinations. (1,2,3 - 1,3,2,- 2,1,3 - 2,3,1, - 3,1,2 - 3,2,1 )
So if the pamphleteer were to select and label the three (previously unlabeled) ciphers completely at random he would still have a
1/6 (or 16.6%) chance of matching the original author's selection. But - we don't know for certain he did. We can't know for certain until someone positively breaks at least one more of the codes.In fact, the only thing we know for certain is that both men labeled #2 as "2" and there are two possible combinations that contain that. This means that the pamphleteer has a
2/6 chance based upon the evidence that we currently have.
That's a 1/3 probability purely by random chance!
I don't know about you but I don't think that those are unreasonable odds. But there is also more to consider.
Legend states that the box contained a "note" and 3 separate ciphers written on paper. So there are at least three sheets of paper involved but probably 4 or more depending on how much paper was used writing the note. But If the "note" and cipher #1 were written on the same sheet of paper though that changes pamphleteer's odds again up to 50/50 because now he's only guessing at 2 and 3. We can't know for certain about this though as the originals are gone.
One last thought is that we humans are fairly methodical creatures. It's not unreasonable to assume that the original author (Beale ?) would have taken great care of these important papers and placed them carefully in the lock box in (his chosen) order. Is it not also reasonable to assume that upon opening the box that Morriss would preserve the order he found them in ? In turn passing it along to pamphleteer in that same order ? it's quite possible that Beale could "label" the papers in any number of different ways without actually marking them 1,2,3 etc. One easy way would be to use three sheets of paper that are the same width but cut so that each successive page is just slightly but noticeably longer than the previous. They could be mixed thoroughly and almost any adult will reassemble them in the same order with the longest on the bottom "pyramid" style. Lastly to my knowledge no where does it say that the papers were not bound by some means - clip, staples, etc. even just poking a hole in a corner and tying a loop of string around it would preserver the proper order of only a few sheets of paper adequately for the timeline involved with this legend. Of course none of the original characters ever documented something as mundane as staples but. . . . your premise does rest on the fact that these papers were rolling around loose in the lock box which may or may not be true.
A little food for thought -
But being a true believer in the gospel tale, I'm sure you're going to be able to explain to the class how it was possible for the author to be 100% certain he had those ciphers in the correct order simply by arranging them according to their length. And then I'm also certain that you're going to be able to tell us how he knew to do that without any instruction from Beale whatsoever? 
Like a letter to Mr Morriss in 1832 that tells all about how to decode the ciphers? 
