megan:-
Wonder if the UK class system and the non commissioned aircrew of old had a role to play?
You'll have to explain that one, if you don't mind. As has been stated in other posts this was never official, never completely widespread. It was usually an affectionate way of referring to the CO when he wasn't present, as distinct from the unaffectionate way by using his surname. When he was present and being addressed it was usually as "Sir", at least on most Transport Squadrons as Brian48Nav has already said.
The RAF has/had many issues over the years but class distinction was never a major one. As a predominantly technical Service it drew its personnel from all backgrounds and many from humble backgrounds rose to high rank. Rather than being indicative of the UK class system I would suggest that the voluntary use of the term "Boss" shows an acceptance of his/her authority over you that reflects his/her ability rather than any right of birth.