I think maybe I have figured out what is going on. The views are correct but my interpretation of what could be in those layers is wrong (and lacking any other good information, maybe have now guessed my way to success).
The 'inner' layers here are not meant to be signal layers but are power and ground plane fills. The dots are vias leading the top/bottom to those planes. The planes themselves are 100% fills which makes them difficult to see.
It's weird that the dots or holes are in the layer fill colour and the 'planes' are empty/blank/background colour... but whatever.
I can at least now go ahead and confirm that with some checks but it would explain a lot.
[edit]
Yup, have been able to confirm the inner planes are power/ground by beeping out the pads of various decoupling caps to each other, which have no top/bottom connections. They are joined by the inner planes.
Looks like I'm un-stuck, at least for the building work...

- Screenshot 2025-04-09 at 18.17.42.png (3.44 MiB) Viewed 1673 times