I remember back in the day we had a board manufacturer request layer alignment targets on all the layers. They wanted 3 of them, not on a perfect square/rectangle. They described to me the reason for them was when manually aligning artwork during the fabrication process they would help ensure that the artwork wasn’t flipped or rotated.
I’m not sure why they needed that on my boards since they were the ones who panelized my designs for the size sheet of FR4 (or pre-preg) that they used in their fabrication process, and they could have added their own panel targets outside my design. We were, after all, paying $200/layer as an NRE artwork fee… (Maybe it was a known design issue with their pannelizing software that would allow board layers to get moved independently of each other?)
I did get an opportunity at that job to visit one of the board houses to see how they manufactured our 4 layer designs. To ensure the copper layers and machining processes all lined up they did use indexing holes (and a jig with pegs) in the border of their panel outside the customer’s artwork. I forget how they aligned the plastic mask sheets for the photolithography process in preparation to etching.
Granted, this was also back in the mid '90s…