As is well-known, the quire numbers of the VM (which in all probability have been added later) do exhibit some handwriting peculiarities which could provide a good clue as to who wrote them, or at least where they were added.
Here they are:

These are typical 15th century numerals. One of the peculiarities is that ‘quartus’ doesn’t have a ‘t’ while ‘quintus’ and ‘sextus’ both have one.
Another peculiarity is the precise way ‘primus’ is written. The abbreviation for ‘-ri’ is not made with a neat ‘i’ above the ‘p’ as in tidy scripts (here is a 1419 example of that kind, from the Czech region of Bohemia: it is at the end of the first line in red, where moreover the ‘9’ abbreviation for ‘-us’ is not used). Indeed, in the VM it is made with some kind of round accent above a not fully closed ‘p’ and also uses ‘9’ for ‘-us’. Here it is in close-up:

Now you may remember that I have already mentionned (at the end of this post) that a certain 1459 manuscript, named Cod. Sang. 839, which has belonged to the St-Gallen Stiftsbibliothek for a very long time (in fact since before 1712 at the very least, most probably since the end of the 15th century) does have a very similar mark at the top of its f176r. So it is an interesting case to study.
What I’ve worked out since last time, is that it is not an isolated mark there, but in fact f176r to f177r are the table of contents of the book, added by a different hand than the scribe of the main text. That table of content was started with black ink, then resumed with light brown ink and a smaller quill pen. Since the main text has four parts, one finds that person’s abbreviations for primus, secundus, tertius and quartus. Here is how they look like:

(St. Gallen, Stiftsbibliothek, Cod. Sang. 839, from f176r, f176v and f177r.)
So it is quite clear to me that is is not the same person as in the VM: most prominently because the quartus is not abbreviated in the same way, but also because the loopy part of the p in primus is not done in one part as in the VM. One can further tell the two manuscripts apart by looking at those Cod. Sang. 839 pages again: the table of contents also contains page numbers, for instance here are some:

St. Gallen, Stiftsbibliothek, Cod. Sang. 839, from f176r, f176v and f177r.
It is clear that 4, 6 and 8 are done very differently from those in the VM where they have different shapes and orientations. So, definitely not the same person.
Still, the shape of the primus is fine, so one can wonder whether this is typical of some region. The answer seems to be: yes, it is typical from the area around Lake Constance around mid-15th century, so that’s a german-speaking region. Here is my thinking.
First of all, this Cod. Sang. 839 together with Cod. Sang. 840 and Cod. Sang. 841 were written by the same scribe, on the same type of paper, the first two in 1459 the third in 1462, according to Scherrer’s catalogue entry for 841. So far, only Cod. Sang. 839 is available in digital form.
But one very interesting clue about the identity of the person who wrote the table of contents is that, according to this book, the owner of Cod. Sang. 841 was a certain Johannes Lippis, and that he also called himself “hanns lippis”. Now, according to the list of St-Gall charters mentionning the name Lippis, there was indeed a Hans Lippis living at St-Gall in 1426 who was a tanner (=Gerber), and also one in 1441 who in one instance served as a lawyer (=Fürsprech).
Since Lippis is not a common name and since the town itself had around 3000 inhabitants at the time, there’s a fair chance that all are the same person. Assuming that Lippis also owned Cod. Sang. 839 due to their identical scribe and topics, then he wrote that table of contents, implying that at least one person in St-Gall wrote primus that way around 1459-1462. (To confirm this, one should check the Lippis handwriting in Cod. Sang. 841 against the TOC of Cod. Sang. 839.) Presumably the library then acquired them from Lippis, perhaps when he died.
Now, I haven’t found other examples of similarly written primus as quire number or section titles. But within lines of text I have some. For instance, the bottom of f35v of this nice Latin-Mittelalemannisch dictionnary (mittelalemannisch was a continuum of dialects spoken in northen Switzerland and south Germany) written mid-15th century from the area of Lake Constance looks like this:

Primus (indeed erste in germanic languages) is written without abbreviating the ‘-ri’. That’s a miss then, you might think. And yet, on the next page one finds:

where ‘mat. primus’ has the ‘primus’ part abbreviated just as in the VM and St-Gall. So it did occur in that region it seems.
For comparison, here is a 1466 text from Tossignano near Bologna in Italy, where in the second column of f3r one can see that “primus” is not exactly like in the VM, and more importantly the numerals in the text show that modern-looking 5 and 6 were already in use in that region, unlike what’s in either the VM or Cod. Sang. 839.
So to conclude, we might have this St-Gall/Lake Constance region lead concerning the stage when someone wrote the quire numbers. Is that exciting? Well, one nice coïncidence is that the only 15th century Zodiac that I know of where the Sagittarius is depicted as a crossbow wielding warrior (and I’ve gone through dozens online), is precisely one from Konstanz…
One might even say: wait a minute, if this is correct, here you have this Hans Lippis who:
1) was a tanner — so someone who had easy access to velum ;
2) lived in an area where the abbreviation for primus is similar to that of the VM (so people after his death could have sorted his stuff, for example strange manuscripts, with month names added later in french near Geneva some time later) ;
3) lived in an area where people sometimes used a crossbowman for Saggitarius ;
4) read about Aristotle’s cosmology and metaphysics — that’s what Cod. Sang. 839 and 840 are about ;
5) was afraid of witches — so says a sentence written by him on f200 of Cod. Sang. 841
6) and lived near one of the largest libraries of the middle-ages (which was full of older Carolingian manuscripts containing decorative gallows and illustrations).
So could he, or a family member, have written the VM as a kind of self-made treatise ? That’s far-fetched certainly, and very probably wrong, but at least not as far-fetched as other things I’ve seen.