Commander in Chief actually goes back to the English Civil War (where Charles Howard was commissioned as lieutenant-general and commander-in-chief); and ‘in chief’ goes back to earlier french, basically denoting a feudal landholding that was given directly by the king.

Keep in mind that a Commander in Chief- while frequently the head of state; historically wasn’t always so. Colonial or Regional Governors were given command of military forces in their areas of authority- that is to say, commissioned as commanders with sole authority over all forces directly by the king. that is to say, they were commissioned as commanders in chief.