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.

A lot of military rank terms derive from French. In French grammar, the noun modifier often goes after the thing it is modifying rather than before.

Chief Commander sounds so much better, although it also brings to mind the image of a stoner superhero: Kief Commander

might be a translation from spanish (not that it clears anything up): comandante en jefe

It's slang for military butt sex.