Is there any protocols to identify what sort of document MS-408 is?

[oshfdk]

They say its been around for 600 years.  Would that be plenty of time to at least identify the properties of the document, so the users could target a cipher for that structure?

Absolutely, yes. There should have been plenty of time to identify what kind of manuscript it is, what it's about and which party/group/sect/cult/profession/individual is responsible for creating it, etc. It's not totally clear what the manuscript has been up to for the whole 600 years, but at least for the past 100 years I'd say all the right people have seen it and a lot of tests have been performed, so normally, yes, by now we would have a very good idea about what it is.

Except, we don't and this is the very reason why this forum exists and why the manuscript is included in the list of the most mysterious artifacts and people discuss some weirdest scenarios.

Can we agree it's a conlang with low entropy, yes or no?

We can't. And it doesn't look like a conlang to me at all.

Do you think a document that has repeatable words at the rate of the MS-408 borders on gibberish?

No, I don't.