The Voynich Manuscript is a cipher because...?

[-JKP-]

Of your three points in favour of a cipher, I agree that point 2) is good. But point 1) is ambiguous, and point 3) is incredibly thin.

Point 3) is not that thin when we begin to consider possibilities of what this label may stand for. Every possibility yields quite strange outcome. Like, if it stands for a number, then from the viewpoint of an unknown language we should admit not only unknown script, but also an unknown numbering system. If it is a noun, then we have a one-letter  noun (is that at all possible in a non-hyeroglyphic script?) And so on.

I don't know if the behavior of the labels in the VMS will be a good model for how the main text works. They may use a different system.