what is your personal theory on what the VM is?

[Koen G]

probably more inclined towards paganism rather than Christianity

I always wonder what people have in mind when they propose something like this. It would be very uncommon for someone in the European Middle Ages to not follow one of the major religions. Tensions existed between religions, not between religious and a-religious. Wrongdoers were those who believed in Jehovah or Allah instead of God. Or who believed in the right God but not in the right way.

Now there were people, both intellectuals and commoners, who were perhaps not participating too enthusiastically in the activities of the Church. People who just weren't that into the whole religion thing, who may have struggled with some questions of the faith even. Who may have secretly harbored thoughts that we would now call "atheism". Keeping in mind that the baseline of society would have been something we would today describe as religious extremism, those people would have been outliers, of course.

But what is this unnamed "paganism" that apparently replaces Christianity? Did this person invent their own belief system? Did they get inspiration somewhere? Were they from a culture that was already paganistic and had an established belief system? Which are its thoughts and how are they expressed? If the female figures are used metaphorically, would they really have offended church authorities? A lot was permitted under the flag of allegory.

There are very few (if any) signs of Christianity in the VM. This is remarkable with its hundreds of human figures. But there are also no farmers, fishermen, kings or queens (the crowned women cannot be literal queens since they are nude). No musicians, jesters, servants, warriors... Well, there is one archer, but he represents a month, not a person. The figures don't interact meaningfully with their environment. They may hold objects, but never use them. They hardly interact with each other, bar a few instances. 

Anyway, I think the meaning of the "nymphs" is much more likely to be metaphorical rather than pagan. If the figures are allegorical, they would connect to a well-established and uninterrupted tradition that goes back to ancient times. If they represent pagan spirits they connect to... well, I don't quite know, that is my question.

edit: just to add, all the known traditions the VM likely drew on had older roots, but were not perceived as "pagan" or anti-Christian. The medicinal properties of plants were respected, and one was allowed to use plant books. Some years ago I studied the case of the Juliana Anicia Codex, an ancient herbal which was maintained, copied and used in a Christian monastery. One was allowed to study the stars, and the Aratea was a popular subject in Latin class. The Balneis tradition was as far as I know also not considered anti-Christian or pro-Pagan...