So, why would they leave scaffolding holes? It just doesn't make any sense.
You are absolutley right. But there is a great sence in it. I try to explain it.
If somebody is looking for the secrets in the painting, he must find an opening- a start, the beginning of the line.
The painter show us the starting point, with a nonsence, or a fail. They draw a detail, which is wrong. This shall catch your mind to the starting point. For a master builder are scaffold holes inside a kathedral a "no go", just as you and me found out.
scaffold holes in that place are a sighn that they just worked on that place on the triforium and they have not finished, because the holes are not closed.
Together with this fact and our searching to find a door in the triforium are the scaffold holes the beginning of the tracks (the beginning of the line).
If we are looking for a door in the outside wall of the triforium and we want to open that door, we need a scaffold, because it is not possible to reach this place without it.
The last step is to transform this facts in an abstract level. "the saffold holes are carring us to the door" and together with the order to mirror something (the light is inverted, ... to calculate against the light) we came to the idea that the scaffold holes are points on the painting which are showing the positions of the three mirror axises. The fourth axis is running through her "right" eye. The "right" eye is a metapher for looking the right way.
This is the way it works and the results are great. You can see that she opend a curtain on her breast (in the altitude of the triforium) which is marked with a sign "M". Wich are the initials of the pope !
Again : the painters give us a help to find the beginning of the track, by painting somthing wrong, which only a person with the right knowledge can find out.
I hope I could help you