[Design of Marci Letter]

[asteckley]

Not every question is answerable. As medievalists, we learn to live with that. We're likely never going to know FOR SURE if and how the Marci letter was attached or associated with the VMS. We're certainly unlikely to learn what made that smudge (maybe Umberto Eco had some pollen on his thumb when he examined it). Sometimes we just have to learn to live with uncertainty.

It is worth noting that literally EVERY MEDIEVAL MANUSCRIPT that is no longer in its place of origin has gaps in provenance and unidentified stains and human interventions in its structure. Those uncertainties do not mean that we must question the authenticity of all of these manuscripts. Occan's Razor applies. 
...

It would be extremely difficult, if not impossible, to formulate a timeline that would explain every stain and fold and hole. But of course if you want to try, I truly hope you are successful!

I'm sure you don't mean to, but it really sounds like you are advocating for "Don't ask questions, because the answers don't matter".  But there are good reasons why these questions are worth answering. 

Einstein supposedly said that everything should be as simple as it can be, but not simpler. He actually said something more along the lines of: everything should be as as simple as possible while still explaining all of the data.

The problem with the scenario that you suggest as being most plausible is that it simply doesn't explain all the data -- it still leaves some some outstanding issues.  Why did Wilfrid say it was "attached" if it wasn't?  Why was it called a "flyleaf"?  Why did he not talk about it for a decade after obtaining it when the content was directly relevant to his claim about the manuscript being the work of Roger Bacon (and there was basically no other evidence to support that claim)?

Do the answers matter to the bigger picture of the Voynich? Absolutely!
Suppose we were to find clear evidence that the letter had once been physically attached to the codex? Suppose, for example, that the endleaf at the end of the codex has the very same watermark as the Marci Letter? (I doubt it does, but no one can say without asking such a question and actually looking for the answer). For one thing, such findings could change the claims about the Jesuit's having done the current binding. More importantly, if the letter is finally positively connected to the Voynich Manuscript then it would put to rest the entire Book Switch Theory and give much more solid support to the putative provenance story.

On the other hand, if another codex were discovered with physical traces—paste marks, stains, or other indicators—showing it had originally contained the Marci Letter, then that would cause the entire provenance story for the manuscript prior to 1911 to collapse.  

These possibilities aren’t trivial. They may indeed never be answered, but whether or not people are inclined to engage with them, they remain relevant.