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

[ololololo]

It would probably be of higher complexity than common ciphers from the time period.

You can do something similar by simply using You are not allowed to view links. Register or Login to view.. For example, the simplest cipher is to replace numbers with Voynichese letters. Here's what I got when I encrypted Lorem ipsum:
okeo okaiin chor cphdy daiin cheor chedan ol chd chey chol sheol oiin dan oro raiin oteaiin chor sheor cphy qo otey dan shdan...
This is far from perfect and is not an exact reproduction of the VMS text, but I think it is somewhat similar, and the cipher reproduces the features of Voynichese.

I think the "monosyllabic tonal language" theory is the most plausible version of this

First of all, it's unclear what kind of language it is. Secondly, it is assumed that the language is recorded using some author's method. Thirdly, if we try to find similarities, we won't get very far...