OP:-
Does anyone know where/when the practice of calling an RAF Squadron Commander 'The Boss' originated?
Whenever it originated it was when Squadron/Unit Commanders of the Royal Air Force had real powers of command. It was certainly so in my time (60's) and as has been already said may well date back to the very origins of the Service. I would humbly suggest that continual use of the term today is simply traditional, such powers having been greatly reduced these days.