Those boxes lined with green felt were grey in colour and were indeed pencil boxes, marked 6B/472 on the top. They were issued with standard RAF nav bags (you can see them by the students' left legs) and fitted into a specially designed pocket in the bag.
The nav bag also included a stowage for the RAF nav ruler, but I found it easier to shorten the nav ruler and stow it inside the bag.
All were excellent pieces of kit!