The first Warrant officers were in the Royal Navy. Command of ships was given to members of the aristocracy by a Royal Commission. Unfortunately, they couldn't actually sail the ships and so they employed professional seamen to do the actual sailing. These professional officers came to be appointed by Royal Warrant. During Nelson's time they were also the only permanent members of a ship's complement. Everyone else only remained on the ship for the duration of a commission, ie between refits.
The use of the term Mister probably comes from the polite mode of address by aristocrats for professional people, ie Master or Mister. They were still officers to everyone else on board for which Sir was appropriate.
As mentioned before; largely the result of tradition rather than design. The Army and then the RAF simply followed long.