Exactly as you say, referring to the club how Everton works, not the manager but the club. It's a different club now to when Bill was in charge. Managers don't sell players per say, the owners/chairman do. It's not like the football manager computer game where you are basically the manager and the owner all in one.
Did Roberto sell Fellaini to Man Utd or did Bill Kenwright sell him to Man Utd? Managers do have a say in outgoing transfers in alot of clubs. Not all and they most definitely don't have the final say. Alex Ferguson, Arsene Wenger maybe being the exceptions.
Unless Branthwaithe forces a move I'd bet my bottom dollar on him being an Everton player next season